Compositions, devices, systems, and methods for using a nanopore

ABSTRACT

The invention herein disclosed provides for devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore. The devices and methods are also used to determine rapidly (˜&gt;50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.

The present application claims priority to and benefits of thefollowing: U.S. Provisional Patent Application Ser. No. 60/921,787entitled “Methods To Limit Enzyme Activity To One Molecule Or ComplexUsing A Nanopore”, filed 4 Apr. 2007, U.S. Provisional PatentApplication Ser. No. 60/931,115 entitled “Methods For SequencingPolynucleotides By Synthesis Using A Nanopore”, filed 21 May, 2007, U.S.Provisional Patent Application Ser. No. 60/962,530 entitled “Methods ForPositioning Single Molecules At A Defined Site” filed 30 Jul. 2007, U.S.Provisional Patent Application Ser. No. 60/967,539 entitled “Methods ForManufacture Of Very Large Scale Arrays Of Independently AddressableNanopores And Methods For Their Use”, filed 4 Sep. 2007, and U.S.Provisional Patent Application Ser. No. 61/062,391 entitled “FeedbackControl Of A Single Tethered Polynucleotide Suspended In A Nanopore ToRepeatedly Probe Polynucleotide-Binding Proteins”, filed 25 Jan., 2008,all of which are herein incorporated by reference in their entirety forall purposes.

This invention was made partly using funds from the National HumanGenome Research Institute grant numbers HG003703-01 and HG004035-01, andfrom the National Institute of General Medical Sciences grant numberGM073617-01A1. The US Federal Government has certain rights to thisinvention.

FIELD OF THE INVENTION

The invention herein disclosed provides for devices and methods that canregulate the time at which an individual polymer in a mixture is actedupon by another compound, for example, an enzyme. The invention is ofparticular use in the fields of molecular biology, structural biology,cell biology, molecular switches, molecular circuits, and molecularcomputational devices, and the manufacture thereof. The invention alsorelates to methods of using the compositions to diagnose whether asubject is susceptible to cancer, autoimmune diseases, cell cycledisorders, or other disorders.

BACKGROUND

The invention relates to the field of compositions, methods, andapparatus for characterizing polynucleotides and other polymers.

Determining the nucleotide sequence of DNA and RNA in a rapid manner isa major goal of researchers in biotechnology, especially for projectsseeking to obtain the sequence of entire genomes of organisms. Inaddition, rapidly determining the sequence of a polynucleotide isimportant for identifying genetic mutations and polymorphisms inindividuals and populations of individuals.

Nanopore sequencing is one method of rapidly determining the sequence ofpolynucleotide molecules. Nanopore sequencing is based on the propertyof physically sensing the individual nucleotides (or physical changes inthe environment of the nucleotides (that is, for example, an electriccurrent)) within an individual polynucleotide (for example, DNA and RNA)as it traverses through a nanopore aperture. In principle, the sequenceof a polynucleotide can be determined from a single molecule. However,in practice, it is preferred that a polynucleotide sequence bedetermined from a statistical average of data obtained from multiplepassages of the same molecule or the passage of multiple moleculeshaving the same polynucleotide sequence. The use of membrane channels tocharacterize polynucleotides as the molecules pass through the small ionchannels has been studied by Kasianowicz et al. (Proc. Natl. Acad. Sci.USA. 93:13770-13773, 1996, incorporate herein by reference) by using anelectric field to force single stranded RNA and DNA molecules through a1.5 nanometer diameter nanopore aperture (for example, an ion channel)in a lipid bilayer membrane. The diameter of the nanopore aperturepermitted only a single strand of a polynucleotide to traverse thenanopore aperture at any given time. As the polynucleotide traversed thenanopore aperture, the polynucleotide partially blocked the nanoporeaperture, resulting in a transient decrease of ionic current. Since thelength of the decrease in current is directly proportional to the lengthof the polynucleotide, Kasianowicz et al. (1996) were able to determineexperimentally lengths of polynucleotides by measuring changes in theionic current.

Baldarelli et al. (U.S. Pat. No. 6,015,714) and Church et al. (U.S. Pat.No. 5,795,782) describe the use of nanopores to characterizepolynucleotides including DNA and RNA molecules on a monomer by monomerbasis. In particular, Baldarelli et al. characterized and sequenced thepolynucleotides by passing a polynucleotide through the nanoporeaperture. The nanopore aperture is imbedded in a structure or aninterface, which separates two media. As the polynucleotide passesthrough the nanopore aperture, the polynucleotide alters an ioniccurrent by blocking the nanopore aperture. As the individual nucleotidespass through the nanopore aperture, each base/nucleotide alters theionic current in a manner that allows the identification of thenucleotide transiently blocking the nanopore aperture, thereby allowingone to characterize the nucleotide composition of the polynucleotide andperhaps determine the nucleotide sequence of the polynucleotide.

One disadvantage of previous nanopore analysis techniques is controllingthe rate at which the target polynucleotide is analyzed. As described byKasianowicz, et al. (1996), nanopore analysis is a useful method forperforming length determinations of polynucleotides. However, thetranslocation rate is nucleotide composition dependent and can rangebetween 10⁵ to 10⁷ nucleotides per second under the measurementconditions outlined by Kasianowicz et al. (1996). Therefore, thecorrelation between any given polynucleotide's length and itstranslocation time is not straightforward. It is also anticipated that ahigher degree of resolution with regard to both the composition andspatial relationship between nucleotide units within a polynucleotidecan be obtained if the translocation rate is substantially reduced.

There is currently a need to provide compositions and methods that canbe used in characterization of polymers, including polynucleotides andpolypeptides, as well as diagnosis and prognosis of diseases anddisorders.

BRIEF DESCRIPTION OF THE INVENTION

The invention provides thin film devices and methods for using the same.The subject devices comprise cis and trans chambers connected by anelectrical communication means. The cis and trans chambers are separatedby a thin film comprising at least one pore or channel. In one preferredembodiment, the thin film comprises a compound having a hydrophobicdomain and a hydrophilic domain. In a more preferred embodiment, thethin film comprises a phospholipid. The devices further comprise a meansfor applying an electric field between the cis and the trans chambers.The pore or channel is shaped and sized having dimensions suitable forpassaging a polymer. In one preferred embodiment the pore or channelaccommodates a part but not all of the polymer. In one other preferredembodiment, the polymer is a polynucleotide. In an alternative preferredembodiment, the polymer is a polypeptide. Other polymers provided by theinvention include polypeptides, phospholipids, polysaccharides, andpolyketides.

In one embodiment, the thin film further comprises a compound having abinding affinity for the polymer. In one preferred embodiment thebinding affinity (K_(a)) is at least 10⁶ l/mole. In a more preferredembodiment the K_(a) is at least 10⁸ l/mole. In yet another preferredembodiment the compound is adjacent to at least one pore. In a morepreferred embodiment the compound is a channel. In a yet more preferredembodiment the channel has biological activity. In a most preferredembodiment, the compound comprises the pore.

In one embodiment the compound comprises enzyme activity. The enzymeactivity can be, for example, but not limited to, enzyme activity ofproteases, kinases, phosphatases, hydrolases, oxidoreductases,isomerases, transferases, methylases, acetylases, ligases, lyases, andthe like. In a more preferred embodiment the enzyme activity can beenzyme activity of DNA polymerase, RNA polymerase, endonuclease,exonuclease, DNA ligase, DNase, uracil-DNA glycosidase, ribosomes,kinase, phosphatase, methylase, acetylase, or the like.

In another embodiment the pore is sized and shaped to allow passage ofan activator, wherein the activator is selected from the groupconsisting of ATP, NAD⁺, NAD⁺, diacylglycerol, phosphatidylserine,eicosinoids, retinoic acid, calciferol, ascorbic acid, neuropeptides,enkephalins, endorphins, 4-aminobutyrate (GABA), 5-hydroxytryptamine(5-HT), catecholamines, acetyl CoA, S-adenosylmethionine, and any otherbiological activator.

In yet another embodiment the pore is sized and shaped to allow passageof a cofactor, wherein the cofactor is selected from the groupconsisting of Mg²⁺, Mn²⁺, Ca²⁺, ATP, NAD⁺, NADP⁺, and any otherbiological cofactor.

In a preferred embodiment the pore or channel is a pore molecule or achannel molecule and comprises a biological molecule, or a syntheticmodified molecule, or altered biological molecule, or a combinationthereof. Such biological molecules are, for example, but not limited to,an ion channel, a nucleoside channel, a peptide channel, a sugartransporter, a synaptic channel, a transmembrane receptor, such as GPCRsand the like, a nuclear pore, synthetic variants, chimeric variants, orthe like. In one preferred embodiment the biological molecule isα-hemolysin.

In an alternative, the compound comprises non-enzyme biologicalactivity. The compound having non-enzyme biological activity can be, forexample, but not limited to, proteins, peptides, antibodies, antigens,nucleic acids, peptide nucleic acids (PNAs), locked nucleic acids(LNAs), morpholinos, sugars, lipids, glycophosphoinositols,lipopolysaccharides or the like. The compound can have antigenicactivity. The compound can have selective binding properties whereby thepolymer binds to the compound under a particular controlledenvironmental condition, but not when the environmental conditions arechanged. Such conditions can be, for example, but not limited to, changein [H⁺], change in environmental temperature, change in stringency,change in hydrophobicity, change in hydrophilicity, or the like.

In another embodiment, the invention provides a compound, wherein thecompound further comprises a linker molecule, the linker moleculeselected from the group consisting of a thiol group, a sulfide group, aphosphate group, a sulfate group, a cyano group, a piperidine group, anFmoc group, and a Boc group.

In one embodiment the thin film comprises a plurality of pores. In oneembodiment the device comprises a plurality of electrodes.

Polymers

In another embodiment, the invention provides a method for controllingbinding of an enzyme to a polymer, the method comprising: providing twoseparate, adjacent pools of a medium and an interface between the twopools, the interface having a channel so dimensioned as to allowsequential monomer-by-monomer passage from one pool to the other pool ofonly one polymer at a time; providing an enzyme having binding activityto a polymer; introducing the polymer into one of the two pools;introducing the enzyme into one of the two pools; applying a potentialdifference between the two pools, thereby creating a first polarity;reversing the potential difference a first time, thereby creating asecond polarity; reversing the potential difference a second time tocreate the first polarity, thereby controlling the binding of the enzymeto the polymer. In a preferred embodiment, the medium is electricallyconductive. In a more preferred embodiment, the medium is an aqueoussolution. In another preferred embodiment, the method further comprisesthe steps of measuring the electrical current between the two pools;comparing the electrical current value (I₁) obtained at the first timethe first polarity was induced with the electrical current value (I₂)obtained at the time the second time the first polarity was induced; anddetermining the difference between I₁ and I₂ thereby obtaining adifference value d1. In another preferred embodiment the method furthercomprises the steps of measuring the electrical current between the twopools; comparing the electrical current value (I₁) obtained at the firsttime the first polarity was induced with the electrical current value(I₂) obtained at a later time and determining the difference between I₁and I₂ thereby obtaining a difference value dI. In a more preferredembodiment, the enzyme is selected from the group consisting ofproteases, kinases, phosphatases, hydrolases, oxidoreductases,isomerases, transferases, methylases, acetylases, ligases, and lyases.In another alternative embodiment, the method further comprises thesteps of providing reagents that initiate enzyme activity; introducingthe reagents to the pool comprising the polynucleotide complex; andincubating the pool at a suitable temperature. In a more preferredembodiment, the reagents are selected from the group consisting of anactivator and a cofactor. In a yet more preferred embodiment, theactivator is introduced into the pool prior to introducing the cofactor.In a yet still further more preferred embodiment, the activator isselected from the group consisting of ATP, NAD⁺, NADP⁺, diacylglycerol,phosphatidylserine, eicosinoids, retinoic acid, calciferol, ascorbicacid, neuropeptides, enkephalins, endorphins, 4-aminobutyrate (GABA),5-hydroxytryptamine (5-HT), catecholamines, acetyl CoA, andS-adenosylmethionine. In another still more preferred embodiment, thecofactor is selected from the group consisting of Mg²⁺, Mn²⁺, Ca²⁺, ATP,NAD⁺, and NADP⁺. In another more preferred embodiment, the polymer isselected from the group consisting of polynucleotides, polypeptides,phospholipids, polysaccharides, and polyketides. In one embodiment theenzyme is introduced into the same pool as the polymer. In analternative embodiment, the enzyme is introduced into the opposite pool.

Polynucleotides

In another embodiment, the invention provides a method for controllingbinding of an enzyme to a partially double-stranded polynucleotidecomplex, the method comprising: providing two separate, adjacent poolsof a medium and an interface between the two pools, the interface havinga channel so dimensioned as to allow sequential monomer-by-monomerpassage from one pool to the other pool of only one polynucleotide at atime; providing an enzyme having binding activity to a partiallydouble-stranded polynucleotide complex; providing a polynucleotidecomplex comprising a first polynucleotide and a second polynucleotide,wherein a portion of the polynucleotide complex is double-stranded, andwherein the first polynucleotide further comprises a moiety that isincompatible with the second polynucleotide; introducing thepolynucleotide complex into one of the two pools; introducing the enzymeinto one of the two pools; applying a potential difference between thetwo pools, thereby creating a first polarity; reversing the potentialdifference a first time, thereby creating a second polarity; reversingthe potential difference a second time to create the first polarity,thereby controlling the binding of the enzyme to the partiallydouble-stranded polynucleotide complex. In a preferred embodiment, themedium is electrically conductive. In a more preferred embodiment, themedium is an aqueous solution. In a preferred embodiment, the moiety isselected from the group consisting of a peptide nucleic acid, a2′-O-methyl group, a fluorescent compound, a derivatized nucleotide, anda nucleotide isomer. In another preferred embodiment, the method furthercomprises the steps of measuring the electrical current between the twopools; comparing the electrical current value obtained at the first timethe first polarity was induced with the electrical current valueobtained at the time the second time the first polarity was induced. Inanother preferred embodiment the method further comprises the steps ofmeasuring the electrical current between the two pools; comparing theelectrical current value obtained at the first time the first polaritywas induced with the electrical current value obtained at a later time.In a more preferred embodiment, the enzyme is selected from the groupconsisting of DNA polymerase, RNA polymerase, endonuclease, exonuclease,DNA ligase, DNase, uracil-DNA glycosidase, kinase, phosphatase,methylase, and acetylase. In another alternative embodiment, the methodfurther comprises the steps of providing at least one reagent thatinitiates enzyme activity; introducing the reagent to the poolcomprising the polynucleotide complex; and incubating the pool at asuitable temperature. In a more preferred embodiment, the reagent isselected from the group consisting of a deoxyribonucleotide and acofactor. In a yet more preferred embodiment, the deoxyribonucleotide isintroduced into the pool prior to introducing the cofactor. In anotherstill more preferred embodiment, the cofactor is selected from the groupconsisting of Mg²⁺, Mn²⁺, Ca²⁺, ATP, NAD⁺, and NADP⁺. In one embodimentthe enzyme is introduced into the same pool as the polynucleotide. In analternative embodiment, the enzyme is introduced into the opposite pool.

Polypeptides

In another embodiment, the invention provides a method for controllingbinding of an enzyme to a polypeptide, the method comprising: providingtwo separate, adjacent pools of a medium and an interface between thetwo pools, the interface having a channel so dimensioned as to allowsequential monomer-by-monomer passage from one pool to the other pool ofonly one polypeptide at a time; providing an enzyme having bindingactivity to a polypeptide; providing a polypeptide comprising amodifiable amino acid residue; introducing the polypeptide into one ofthe two pools; introducing the enzyme into one of the two pools;applying a potential difference between the two pools, thereby creatinga first polarity; reversing the potential difference a first time,thereby creating a second polarity; reversing the potential difference asecond time to create the first polarity, thereby controlling thebinding of the enzyme to the polypeptide. In a preferred embodiment, themedium is electrically conductive. In a more preferred embodiment, themedium is an aqueous solution. In a preferred embodiment, the moiety isselected from the group consisting of a peptide nucleic acid, a2′-O-methyl group, a fluorescent compound, a derivatized nucleotide, anda nucleotide isomer. In another preferred embodiment, the method furthercomprises the steps of measuring the electrical current between the twopools; comparing the electrical current value obtained at the first timethe first polarity was induced with the electrical current valueobtained at the time the second time the first polarity was induced. Inanother preferred embodiment the method further comprises the steps ofmeasuring the electrical current between the two pools; comparing theelectrical current value obtained at the first time the first polaritywas induced with the electrical current value obtained at a later time.In a more preferred embodiment, the enzyme is selected from the groupconsisting of DNA polymerase, RNA polymerase, endonuclease, exonuclease,DNA ligase, DNase, uracil-DNA glycosidase, kinase, phosphatase,methylase, and acetylase. In another alternative embodiment, the methodfurther comprises the steps of providing at least one reagent thatinitiates enzyme activity; introducing the reagent to the poolcomprising the polynucleotide complex; and incubating the pool at asuitable temperature. In a more preferred embodiment, the reagent isselected from the group consisting of an activator and a cofactor. In amost preferred embodiment, the activator is selected from the groupconsisting of ATP, NAD⁺, NADP⁺, diacylglycerol, phosphatidylserine,acetyl CoA, and S-adenosylmethionine. In a yet more preferredembodiment, the activator is introduced into the pool prior tointroducing the cofactor. In another still more preferred embodiment,the cofactor is selected from the group consisting of Mg²⁺, Mn²⁺, Ca²⁺,ATP, NAD⁺, and NADP⁺. In one embodiment the enzyme is introduced intothe same pool as the polypeptide. In an alternative embodiment, theenzyme is introduced into the opposite pool.

The invention herein disclosed provides for devices and methods that canregulate the rate at which an individual polymer in a mixture is actedupon by another compound, for example, an enzyme. The devices andmethods are also used to determine the nucleotide base sequence of apolynucleotide The invention is of particular use in the fields ofmolecular biology, structural biology, cell biology, molecular switches,molecular circuits, and molecular computational devices, and themanufacture thereof.

In one alternative embodiment, the invention provides a method forcontrolling binding of an enzyme to a partially double-strandedpolynucleotide complex and the method resulting in identifying thesequence of a polynucleotide, the method comprising the steps of:providing two separate adjacent pools comprising a medium, an interfacebetween the two pools, the interface having a channel so dimensioned asto allow sequential monomer-by-monomer passage from the cis-side of thechannel to the trans-side of the channel of only one polynucleotidestrand at a time; providing an enzyme having binding activity to apartially double-stranded polynucleotide complex; providing at least oneprotected deoxyribonucleotide, the protection comprising using aprotecting moiety; providing an annealing agent; providing apolynucleotide complex comprising a first polynucleotide and a secondpolynucleotide, wherein a portion of the polynucleotide complex isdouble-stranded and a portion is single-stranded; introducing thepolynucleotide complex into one of the two pools; applying a potentialdifference between the two pools, thereby creating a first polarity, thefirst polarity causing the single stranded portion of the polynucleotideto transpose through the channel to the trans-side; introducing theenzyme and the protected deoxyribonucleotide into the same pool;introducing the annealing agent into the other pool; allowing theannealing agent to bind to the single-stranded polynucleotide; allowingthe enzyme and the protected deoxyribonucleotide to bind to thepolynucleotide; allowing the protected deoxyribonucleotide to beincorporated into the polynucleotide; reversing the potential differencea first time, thereby creating a second polarity; allowing the protecteddeoxyribonucleotide to release the protecting moiety and becomedeprotected; measuring the abundance of the protecting moiety; reversingthe potential difference a second time to create the first polarity;repeating any one of the steps, thereby controlling the binding of theenzyme to the double-stranded polynucleotide complex and determining thesequence of the polynucleotide. In a preferred embodiment, the medium iselectrically conductive. In a more preferred embodiment, the medium isan aqueous medium. In one preferred embodiment, the moiety is selectedfrom the group consisting of a peptide nucleic acid, a 2′-O-methylgroup, a fluorescent compound, anthocyanins, green fluorescent protein(GFP), β-glucuronidase, luciferase, Cy3, Cy5, a derivatized nucleotide,and a nucleotide isomer. In another preferred embodiment, the enzyme isselected from the group consisting of DNA polymerase, RNA polymerase,endonuclease, exonuclease, DNA ligase, DNase, uracil-DNA glycosidase,kinase, phosphatase, methylase, and acetylase. In one alternativeembodiment, the method further comprises the steps of measuring theelectrical current between the two pools; comparing the electricalcurrent value obtained at the first time the first polarity was inducedwith the electrical current value obtained at the time the second timethe first polarity was induced. In another alternative embodiment, themethod further comprises the steps of measuring the electrical currentbetween the two pools; comparing the electrical current value obtainedat the first time the first polarity was induced with the electricalcurrent value obtained at a later time. In a yet further alternativeembodiment, the method further comprises the steps of providing at leastone reagent that initiates enzyme activity; introducing the reagent tothe pool comprising the polynucleotide complex; and incubating the poolat a temperature sufficient to maintain enzyme activity. In a preferredembodiment, the reagent is a cofactor. In a more preferred embodiment,the cofactor is selected from the group consisting of Mg²⁺, Mn²⁺, Ca²⁺,ATP, NAD⁺, NADP⁺, and S-adenosylmethionine. In another preferredembodiment, the protected deoxyribonucleotide comprises adeoxyribonucleotide selected from the group consisting of dATP, dGTP,dTTP, dCTP, and dUTP. In another more preferred embodiment, the reagentis selected from the group consisting of ddATP, ddGTP, ddTTP, ddCTP, andddUTP. In a yet other preferred embodiment, the aqueous medium of atleast one pool comprises an annealing agent. In a more preferredembodiment, the annealing agent selected from the group consisting of acomplementary oligonucleotide and streptavidin.

The invention also provides a method for sensing the position of amolecule relative to a pore, the method comprising: providing twoseparate, adjacent pools of a medium and a structure between the twopools, the structure having an ion-permeable pore; providing a polyion;providing a molecule having binding activity to the polyion; introducingthe polyion into one of the two pools; introducing the molecule into thesame pool; applying a potential difference between the two pools,thereby creating a first polarity; measuring a first electrical currentbetween the two pools, thereby sensing the position of a moleculerelative to the pore. In a preferred embodiment, the molecule is amacromolecule, wherein the macromolecule selected from the groupconsisting of proteases, kinases, phosphatases, hydrolases,oxidoreductases, isomerases, transferases, methylases, acetylases,ligases, lyases, a transmembrane receptor, a receptor tyrosine kinase, aT-cell receptor, an MHC receptor, and a nuclear receptor. In anotherpreferred embodiment the medium is electrically conductive. In a morepreferred embodiment, the medium is an aqueous solution. In anotherpreferred embodiment, the structure further comprises a compound,wherein the compound is selected from the group consisting of a thiolgroup, a sulfide group, a phosphate group, a sulfate group, a cyanogroup, a piperidine group, an Fmoc group, and a Boc group, siliconnitride, bifunctional alkyl sulfide, and gold. In another preferredembodiment, the polyion is selected from the group consisting ofpolynucleotides, polypeptides, phospholipids, polysaccharides, andpolyketides. In alternative embodiment, the method further comprises thesteps of reversing the potential difference a first time, therebycreating a second polarity; reversing the potential difference a secondtime to create the first polarity, measuring a second electrical currentbetween the two pools, thereby further sensing the position of themolecule relative to the pore. In another alternative embodiment, themethod further comprises the steps of measuring the electrical currentbetween the two pools; comparing the electrical current value obtainedat the first time the first polarity was induced with the electricalcurrent value obtained at a later time. In a still further alternativeembodiment, the method further comprises the steps of providing reagentsthat initiate enzyme activity; introducing the reagents to the poolcomprising the polynucleotide complex; and incubating the pool at asuitable temperature. In a more preferred embodiment, the reagents areselected from the group consisting of an activator and a cofactor. Inanother more preferred embodiment, the activator is introduced into thepool prior to introducing the cofactor. In a still more preferredembodiment, the activator is selected from the group consisting of ATP,NAD⁺, NADP⁺, diacylglycerol, phosphatidylserine, eicosinoids, glycosylphosphatidyl inositols, glycophosphoinositols, lipopolysaccharides,retinoic acid, calciferol, ascorbic acid, neuropeptides, enkephalins,endorphins, 4-aminobutyrate (GABA), 5-hydroxytryptamine (5-HT),catecholamines, acetyl CoA, and S-adenosylmethionine. In another stillmore preferred embodiment, the cofactor is selected from the groupconsisting of Mg²⁺, Mn²⁺, Ca²⁺, ATP, NAD⁺, and NADP⁺.

In a preferred embodiment the pore or channel comprises a biologicalmolecule, or a synthetic modified or altered biological molecule. Suchbiological molecules are, for example, but not limited to, an ionchannel, such as a-hemolysin, a nucleoside channel, a peptide channel, asugar transporter, a synaptic channel, a transmembrane receptor, such asGPCRs, a receptor tyrosine kinase, and the like, a T-cell receptor, anMHC receptor, a nuclear receptor, such as a steroid hormone receptor, anuclear pore, or the like.

In an alternative embodiment, the compound comprises non-enzymebiological activity. The compound having non-enzyme biological activitycan be, for example, but not limited to, proteins, peptides, antibodies,antigens, nucleic acids, peptide nucleic acids (PNAs), locked nucleicacids (LNAs), morpholinos, sugars, lipids, glycosyl phosphatidylinositols, glycophosphoinositols, lipopolysaccharides, or the like. Thecompound can have antigenic activity. The compound can have ribozymeactivity. The compound can have selective binding properties whereby thepolymer binds to the compound under a particular controlledenvironmental condition, but not when the environmental conditions arechanged. Such conditions can be, for example, but not limited to, changein [H⁺], change in environmental temperature, change in stringency,change in hydrophobicity, change in hydrophilicity, or the like.

In one embodiment the macromolecule comprises enzyme activity. Theenzyme activity can be, for example, but not limited to, enzyme activityof proteases, kinases, phosphatases, hydrolases, oxidoreductases,isomerases, transferases, methylases, acetylases, ligases, lyases, andthe like. In a more preferred embodiment the enzyme activity can beenzyme activity of DNA polymerase, RNA polymerase, endonuclease,exonuclease, DNA ligase, DNase, uracil-DNA glycosidase, kinase,phosphatase, methylase, acetylase, glucose oxidase, or the like. In analternative embodiment, the macromolecule can comprise more that oneenzyme activity, for example, the enzyme activity of a cytochrome P450enzyme. In another alternative embodiment, the macromolecule cancomprise more than one type of enzyme activity, for example, mammalianfatty acid synthase. In another embodiment the macromolecule comprisesribozyme activity.

In an alternative embodiment, the macromolecule comprises non-enzymebiological activity. The macromolecule having non-enzyme biologicalactivity can be, for example, but not limited to, proteins, peptides,antibodies, antigens, nucleic acids, peptide nucleic acids (PNAs),locked nucleic acids (LNAs), morpholinos, sugars, phospholipids, lipids,glycosyl phosphatidyl inositols, glycophosphoinositols,lipopolysaccharides, or the like. The macromolecule can havepolynucleotide-binding activity and/or polypeptide biosynthesisactivity, such as, but not limited to, a ribosome or a nucleosome. Themacromolecule can have antigenic activity. The macromolecule can haveselective binding properties whereby the polymer binds to themacromolecule under a particular controlled environmental condition, butnot when the environmental conditions are changed. Such conditions canbe, for example, but not limited to, change in [H⁺], change inenvironmental temperature, change in stringency, change inhydrophobicity, change in hydrophilicity, or the like.

In another embodiment, the invention provides a compound, wherein thecompound further comprises a linker molecule, the linker moleculeselected from the group consisting of a thiol group, a sulfide group, aphosphate group, a sulfate group, a cyano group, a piperidine group, anFmoc group, and a Boc group. In another embodiment the compound isselected from the group consisting of a bifunctional alkyl sulfide andgold.

In one embodiment the thin film comprises a plurality of pores. In oneembodiment the device comprises a plurality of electrodes.

Single-channel thin film devices, systems, and methods for using thesame are provided. The subject devices or systems comprise cis and transchambers connected by an electrical communication means. At the cis endof the electrical communication means is a horizontal conical aperturesealed with a thin film that includes a single nanopore or channel. Thedevices further include a means for applying an electric field betweenthe cis and trans chambers. The subject devices find use in applicationsin which the ionic current through a nanopore or channel is monitored,where such applications include the characterization of naturallyoccurring ion channels, the characterization of polymeric compounds, andthe like.

The invention also provides a method for delivering a singlemacromolecule to a defined nanoscale site specified by a user.

The invention also provides a method for attaching a singlemacromolecule to a defined nanoscale site specified by a user.

The invention also provides a method for monitoring the function of asingle macromolecule (or combination of single molecules) using ioniccurrent through a nanoscopic pore.

The invention also provides a device or system for detecting binding ofat least two compounds, the device comprising a mixed-signalsemiconductor wafer, at least one electrochemical layer, theelectrochemical layer comprising a semiconductor material, wherein thesemiconductor material further comprises a surface modifier, wherein theelectrochemical layer defines a plurality of orifices, the orificescomprising a chamber and a neck and wherein the chamber of the orificesco-localize with a metallization composition of the mixed-signalsemiconductor wafer, wherein a portion of the orifice is plugged with ametal, wherein the metal is in electronic communication with themetallization composition, and wherein the orifice further comprises athin film, the thin film forming a solvent-impermeable seal at the neckof the orifice, the thin film further comprising a pore, the porefurther comprising a pore aperture. In a preferred embodiment, thecompounds are biological compounds. In a more preferred embodiment, thebiological compounds are selected from the group consisting ofpolynucleotides, polypeptides, phospholipids, polysaccharides,polyketides, proteases, kinases, phosphatases, hydrolases,oxidoreductases, isomerases, transferases, methylases, acetylases,ligases, and lyases. In another preferred embodiment, the semiconductormaterial is selected from the group consisting of silicon dioxide(SiO₂), silicon oxy nitride (SiON), silicon nitride (SiN), metal oxide,and metal silicate. In a more preferred embodiment, the semiconductormaterial is silicon dioxide. In another preferred embodiment, thesurface modifier is a hydrocarbon. In a more preferred embodiment, themetallization composition is selected from the group consisting ofnickel, gold, copper, and aluminum. In a most preferred embodiment, themetal is silver. In a preferred embodiment, the thin film is a molecularbilayer. In a more preferred embodiment, the thin film is a phospholipidbilayer. In one alternative embodiment, the orifice is between 0.5 and 3μm in size. In a preferred embodiment, the orifice is between 1 and 2 μmin size. In a most preferred embodiment, the orifice is between 1.25 and1.5 μm in size. In another preferred embodiment, the pore is abiological molecule. In a more preferred embodiment, the biologicalmolecule is selected from the group consisting of an ion channel, anucleoside channel, a peptide channel, a sugar transporter, a synapticchannel, a transmembrane receptor, and a nuclear pore. In a mostpreferred embodiment, the biological molecule is α-hemolysin. In apreferred embodiment, the pore aperture is between about 1 and 10 nm insize. In a more preferred embodiment, the pore aperture is between about1 and 4 nm in size. In a most preferred embodiment, the pore aperture isbetween about 1 and 2 nm in size. In an alternative most preferredembodiment the pore aperture is between about 2 and 4 nm in size.

The invention also provides a finite state machine that can be used todetect and control binding of a molecule to a polymer. In oneembodiment, the molecule is a protein. In a preferred embodiment, theprotein is an enzyme. In one embodiment, the finite state machine candetect a polymer compound having a structural element that inhibitstransposition of the polymer compound through a nanopore. In onepreferred embodiment, the finite state machine can detect a polymercompound comprising a DNA hairpin structure in a nanopore, eject thecompound comprising a DNA hairpin or DNA duplex structure from ananopore after it has been detected but prior to unzipping the hairpinor DNA duplex structure. In an alternative embodiment the polymercompound comprises a derivatized nucleic acid. In yet anotheralternative embodiment, the polymer compound comprises a peptide nucleicacid.

In one embodiment the finite state machine can control binding of amolecule to a polymer at a rate of between about 5 Hz and 2000 Hz. Thefinite state machine can control binding of a molecule to a polymer at,for example, about 5 Hz, at about 10 Hz, at about 15 Hz, at about 20 Hz,at about 25 Hz, at about 30 Hz, at about 35 Hz, at about 40 Hz, at about45 Hz, at about 50 Hz, at about 55 Hz, at about 60 Hz, at about 65 Hz,at about 70 Hz, at about 75 Hz, at about 80 Hz, at about 85 Hz, at about90 Hz, at about 95 Hz, at about 100 Hz, at about 110 Hz, at about 120Hz, at about 125 Hz, at about 130 Hz, at about 140 Hz, at about 150 Hz,at about 160 Hz, at about 170 Hz, at about 175 Hz, at about 180 Hz, atabout 190 Hz, at about 200 Hz, at about 250 Hz, at about 300 Hz, atabout 350 Hz, at about 400 Hz, at about 450 Hz, at about 500 Hz, atabout 550 Hz, at about 600 Hz, at about 700 Hz, at about 750 Hz, atabout 800 Hz, at about 850 Hz, at about 900 Hz, at about 950 Hz, atabout 1000 Hz, at about 1125 Hz, at about 1150 Hz, at about 1175 Hz, atabout 1200 Hz, at about 1250 Hz, at about 1300 Hz, at about 1350 Hz, atabout 1400 Hz, at about 1450 Hz, at about 1500 Hz, at about 1550 Hz, atabout 1600 Hz, at about 1700 Hz, at about 1750 Hz, at about 1800 Hz, atabout 1850 Hz, at about 1900 Hz, at about 950 Hz, and at about 2000 Hz.In a preferred embodiment, the finite state machine can control bindingof a molecule to a polymer at a rate of between about 25 Hz and about250 Hz. In amore preferred embodiment the finite state machine cancontrol binding of a molecule to a polymer at a rate of between about 45Hz and about 120 Hz. In a most preferred embodiment the finite statemachine can control binding of a molecule to a polymer at a rate ofabout 50 Hz.

The invention can be used to determine the nucleotide sequence of apolynucleotide. The invention can also be used to determine the relativeaffinity of an enzyme for binding a polynucleotide, thereby using theinvention to identify novel enzyme compounds that bind topolynucleotides.

In one embodiment, the subject devices or systems comprise cis and transchambers connected by an electrical communication means. The cis andtrans chambers are separated by a thin film comprising at least one poreor channel. In one preferred embodiment, the thin film comprises acompound having a hydrophobic domain and a hydrophilic domain. In a morepreferred embodiment, the thin film comprises a phospholipid. Thedevices further comprise a means for applying an electric field betweenthe cis and the trans chambers. The devices further comprise a means fordetecting the current between the cis and the trans chambers. The poreor channel is shaped and sized having dimensions suitable for passaginga polymer. In one preferred embodiment the pore or channel accommodatesa substantial portion of the polymer. In a yet more preferred embodimentthe pore or channel has biological activity. In another preferredembodiment, the polymer is a polynucleotide.

In one embodiment, the thin film further comprises a compound having abinding affinity for the polymer. In one preferred embodiment thebinding affinity (K_(a)) is at least 10⁶ l/mole. In a more preferredembodiment the K_(a) is at least 10⁸ l/mole. In yet another preferredembodiment the compound is adjacent to at least one pore. In a morepreferred embodiment the compound comprises a polypeptide.

In one embodiment the compound comprises enzyme activity. The enzymeactivity can be, for example, but not limited to, enzyme activity ofproteases, kinases, phosphatases, hydrolases, oxidoreductases,isomerases, transferases, methylases, acetylases, ligases, lyases, andthe like. In a more preferred embodiment the enzyme activity can beenzyme activity of DNA polymerase, RNA polymerase, endonuclease,exonuclease, DNA ligase, DNase, uracil-DNA glycosidase, kinase,phosphatase, methylase, acetylase, or the like.

In another embodiment the pore or channel is sized and shaped to allowpassage of an activator, wherein the activator is selected from thegroup consisting of ATP, NAD⁺, NADP⁺, and any other biologicalactivator.

In yet another embodiment the pore or channel is sized and shaped toallow passage of a cofactor, wherein the cofactor is selected from thegroup consisting of Mg²⁺, Mn²⁺, Ca²⁺, ATP, NAD⁺, NADP⁺, and any otherbiological cofactor.

In a preferred embodiment the pore or channel comprises a biologicalmolecule, or a synthetic modified or altered biological molecule. Suchbiological molecules are, for example, but not limited to, an ionchannel, a nucleoside channel, a peptide channel, a sugar transporter, asynaptic channel, a transmembrane receptor, such as GPCRs and the like,a nuclear pore, or the like. In one preferred embodiment the biologicalmolecule is α-hemolysin.

In an alternative, the compound comprises non-enzyme biologicalactivity. The compound having non-enzyme biological activity can be, forexample, but not limited to, proteins, peptides, antibodies, antigens,nucleic acids, peptide nucleic acids (PNAs), locked nucleic acids(LNAs), morpholinos, sugars, lipids, glycophosphoinositols,lipopolysaccharides, or the like. The compound can have antigenicactivity. The compound can have selective binding properties whereby thepolymer binds to the compound under a particular controlledenvironmental condition, but not when the environmental conditions arechanged. Such conditions can be, for example, but not limited to, changein [H⁺], change in environmental temperature, change in stringency,change in hydrophobicity, change in hydrophilicity, or the like.

In yet another embodiment, the invention provides a method forcontrolling binding of an enzyme to a polynucleotide using voltagefeedback control, the method resulting in repeated capture of anddissociation of the enzyme by the polynucleotide, the method comprisingthe steps of: providing two separate adjacent compartments comprising amedium, an interface between the two compartments, the interface havinga channel so dimensioned as to allow sequential monomer-by-monomerpassage from the cis-side of the channel to the trans-side of thechannel of only one polynucleotide strand at a time; providing an enzymehaving binding activity for a polynucleotide; providing a protecteddeoxyribonucleotide; providing a polynucleotide-binding compound;providing a polynucleotide complex, wherein a portion of thepolynucleotide complex is double-stranded and a portion issingle-stranded; introducing the polynucleotide complex into one of thetwo chambers; applying a potential difference between the two chambers,thereby creating a first polarity, the first polarity causing the singlestranded portion of the polynucleotide to transpose through the channelto the trans-side; introducing the protected deoxyribonucleotide intothe same chamber; introducing the enzyme into the same chamber; allowingthe enzyme to bind to the polynucleotide; allowing the protecteddeoxyribonucleotide to bind to the polynucleotide; measuring theelectrical current through the channel thereby detecting the binding ofthe enzyme and the protected deoxyribonucleotide to the polynucleotide;introducing the polynucleotide-binding compound into the other of thetwo chambers; decreasing the potential difference a first time, therebycreating a second polarity; allowing the polynucleotide-binding compoundto bind to the single-stranded polynucleotide; reversing the potentialdifference, thereby creating a third polarity; reversing the potentialdifference a second time; measuring the electrical current through thechannel, thereby detecting a polynucleotide alone or a polynucleotidebound to the enzyme and the protected deoxyribonucleotide; repeating anyone of the steps, thereby controlling the binding of the enzyme to thepolynucleotide. In a preferred embodiment, the method further comprisesthe steps of measuring the electrical current between the two chambers;comparing the electrical current value obtained at the first time thefirst polarity was induced with the electrical current value obtained atthe time the second time the first polarity was induced. In anotherpreferred embodiment, the method further comprises the steps ofmeasuring the electrical current between the two chambers; comparing theelectrical current value obtained at the first time the first polaritywas induced with the electrical current value obtained at a later time.In a preferred embodiment, the polynucleotide-binding compound isselected from the group consisting of an oligonucleotide complementaryto the polynucleotide, a peptide nucleic acid, a locked nucleic acid, aderivatized nucleotide, and a nucleotide isomer. In another preferredembodiment, the enzyme is selected from the group consisting of DNApolymerase, RNA polymerase, endonuclease, exonuclease, DNA ligase,DNase, uracil-DNA glycosidase, kinase, phosphatase, methylase, andacetylase. In another preferred embodiment the medium is electricallyconductive. In another preferred embodiment the medium is an aqueousmedium. In another preferred embodiment the protecteddeoxyribonucleotide comprises a deoxyribonucleotide selected from thegroup consisting of dATP, dGTP, TTP, dCTP, UTP, and dUTP.

The method may further comprise the steps of providing at least onereagent that initiates enzyme activity; introducing the reagent to thechamber comprising the polynucleotide complex; and incubating thechamber at a temperature sufficient to maintain enzyme activity. In apreferred embodiment the reagent is a cofactor. In a more preferredembodiment, the cofactor is selected from the group consisting of Mg²⁺,Mn²⁺, Ca²⁺, ATP, NAD⁺, NADP⁺, and S-adenosylmethionine. In anotherpreferred embodiment, the reagent is selected from the group consistingof ddATP, ddGTP, ddTTP, ddCTP, and ddUTP.

In another embodiment of the invention, the invention provides a methodfor controlling binding of an enzyme to a polynucleotide using voltagefeedback control, the method resulting in identifying the sequence of apolynucleotide, the method comprising the steps of: providing twoseparate adjacent chambers comprising a medium, an interface between thetwo chambers, the interface having a channel so dimensioned as to allowsequential monomer-by-monomer passage from the cis-side of the channelto the trans-side of the channel of only one polynucleotide strand at atime; providing an enzyme having binding activity for a polynucleotide;providing a protected deoxyribonucleotide; providing apolynucleotide-binding compound; providing a polynucleotide complex,wherein a portion of the polynucleotide complex is double-stranded and aportion is single-stranded; introducing the polynucleotide complex intoone of the two chambers; applying a potential difference between the twochambers, thereby creating a first polarity, the first polarity causingthe single stranded portion of the polynucleotide to transpose throughthe channel to the trans-side; introducing the protecteddeoxyribonucleotide into the same chamber; introducing the enzyme intothe same chamber; allowing the enzyme to bind to the polynucleotide;allowing the protected deoxyribonucleotide to bind to thepolynucleotide; measuring the electrical current through the channelthereby detecting the binding of the enzyme and the protecteddeoxyribonucleotide to the polynucleotide; introducing thepolynucleotide-binding compound into the other of the two chambers;decreasing the potential difference a first time, thereby creating asecond polarity; allowing the polynucleotide-binding compound to bind tothe single-stranded polynucleotide; reversing the potential difference,thereby creating a third polarity; reversing the potential difference asecond time; measuring the electrical current through the channel,thereby detecting a polynucleotide alone or a polynucleotide bound tothe enzyme and the protected deoxyribonucleotide; repeating any one ofthe steps, thereby controlling the binding of the enzyme to thepolynucleotide. In a preferred embodiment, the method further comprisesthe steps of measuring the electrical current between the two chambers;comparing the electrical current value obtained at the first time thefirst polarity was induced with the electrical current value obtained atthe time the second time the first polarity was induced. In anotherpreferred embodiment, the method further comprises the steps ofmeasuring the electrical current between the two chambers; comparing theelectrical current value obtained at the first time the first polaritywas induced with the electrical current value obtained at a later time.In a preferred embodiment, the polynucleotide-binding compound isselected from the group consisting of an oligonucleotide complementaryto the polynucleotide, a peptide nucleic acid, a locked nucleic acid, aderivatized nucleotide, and a nucleotide isomer. In another preferredembodiment, the enzyme is selected from the group consisting of DNApolymerase, RNA polymerase, endonuclease, exonuclease, DNA ligase,DNase, uracil-DNA glycosidase, kinase, phosphatase, methylase, andacetylase. In another preferred embodiment the medium is electricallyconductive. In another preferred embodiment the medium is an aqueousmedium. In another preferred embodiment the protecteddeoxyribonucleotide comprises a deoxyribonucleotide selected from thegroup consisting of dATP, dGTP, TTP, dCTP, UTP, and dUTP.

The method may further comprise the steps of providing at least onereagent that initiates enzyme activity; introducing the reagent to thechamber comprising the polynucleotide complex; and incubating thechamber at a temperature sufficient to maintain enzyme activity. In apreferred embodiment the reagent is a cofactor. In a more preferredembodiment, the cofactor is selected from the group consisting of Mg²⁺,Mn²⁺, Ca²⁺, ATP, NADP⁺, NADP⁺, and S-adenosylmethionine. In anotherpreferred embodiment, the reagent is selected from the group consistingof ddATP, ddGTP, ddTTP, ddCTP, and ddUTP.

In one embodiment the thin film comprises a plurality of pores. In oneembodiment the device comprises a plurality of electrodes.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates an embodiment of the invention whereby enzyme bindingto a polynucleotide is prevented by a blocking primer.

FIG. 2 illustrates an embodiment of the invention whereby enzymecatalytic activity upon a polynucleotide is prevented by a blockingprimer.

FIG. 3 illustrates an embodiment of the invention whereby enzymecatalytic activity upon a polynucleotide is activated by injection ofMg²⁺ across the nanopore.

FIG. 4 illustrates an embodiment of the invention showing a method forsequencing single polynucleotide molecules.

FIG. 5 illustrates an embodiment of the invention showing an alternativemethod for sequencing single polynucleotide molecules.

FIG. 6 illustrates an embodiment of the invention showing a method forpositioning single molecules at a defined site.

FIG. 7 illustrates an embodiment of the invention showing an alternativemethod for positioning single molecules at a defined site.

FIG. 8 illustrates an embodiment of the invention showing anotheralternative method for positioning single molecules at a defined site.

FIG. 9 illustrates an exemplary embodiment of how the invention can bemanufactured showing a side cutaway view of two array elements.

FIG. 10 illustrates an overhead perspective of the invention showingportions of four adjacent elements of the invention.

FIG. 11 illustrates a flow chart disclosing the system of one embodimentof the invention.

FIG. 12 illustrates a single α-hemolysin protein channel (mushroomshape) inserted into lipid bilayer. Under applied potential (trans-sidepositive), K⁺ ions flow to the cis side, and Cl⁻ ions flow to the transside. The vestibule and stem of the pore channel are shown.

FIG. 13 illustrates a schematic of nanopore and DNA (top), and plot ofrepresentative ionic current signal (bottom) during a 20 base pairhairpin DNA translocation event under 180 mV applied potential. (I) At180 mV, KCl ions pass through the open channel resulting in ˜64 pAcurrent. (II) Upon capture of the single-stranded end of the DNAmolecule into the cis opening of the pore, the flow of ions is reducedto ˜20 pA. (III) After ˜5 msec, the voltage unzips the hairpin, causingssDNA to pass through the pore into the trans chamber, completing themeasured blockaded event. The duration of the event is referred to asdwell time.

FIG. 14 illustrates Distinguishing DNA, DNA/KF complexes, or DNA/KF/dNTPcomplexes in the nanopore device. Row (a) depicts translocation throughthe nanopore of DNA alone (14 bp hairpin with a 36 nucleotide 5′overhang and 2′-3′ dideoxycytidine terminus, template base at n=0 is C),while translocation of the 14 bphp from complexes with KF, or fromcomplexes with KF and dGTP, are shown in rows (b) and (c), respectively.For each row, a diagram of the nanopore with the associated complex(column I), a current trace (column II), and a dwell time event plot(column III) are presented. In column (IV) probability histograms of thebase 10 logarithm of dwell time data are shown in solid. Closeexamination of the event plot in c, column III reveals that most longdwell time events are within 22 to 24 pA. A open bar subset histogramfor the events within 22 to 24 pA is overlaid on probability histogram(c), revealing that the chosen range is dominated by long dwell timeevents.

FIG. 15 illustrates tethering of a captured DNA oligomer by annealing atrans-side primer. a) The finite-state machine (FSM) monitors the openchannel current for translocation events. b) Captured molecule causesthe current to attenuate, and the FSM diagnoses an event (DNA orDNA/KF/dGTP) based on the threshold [15.75, 26.75] pA. c) Upon eventdiagnosis, the FSM reduces the applied voltage to 50 mV for 20 sec,during which time the 20 mer primer anneals to the 5′ end. The graphicshows a close up of the lower half of nanopore, with the 5′ end and 20mer primer in the trans chamber.

FIG. 16 illustrates a time course of ionic current signal in tetheredDNA experiment. First 2 seconds shows the end of the 20 sec tetheringwaiting period (50 mV applied) for 5′-end primer to anneal in transchamber. Fishing time of t_(fish)=5 seconds used, with nine probe eventsshown. Probe event number 5 is blown-up to show details of anenzyme-bound event, with terminal step and subsequent terminal stepdiagnosis after 1.13 msec. Since enzyme-bound events last ˜100 msec, thecontrol logic is primarily in fishing mode in this experiment.

FIG. 17 illustrates fishing and probing of tethered DNA molecule in ananopore. a) Fishing mode, with t_(fish)=0.521 sec. b) Probing mode, inwhich the FSM applies 150 mV until a DNA alone event is diagnosed withthreshold [7.5, 15.5] pA. In the event shown, DNA alone is diagnosed assoon as the transient settles, with no enzyme bound to the DNA, and thefishing mode is restarted. c) Fishing mode.

FIG. 18 illustrates another method for fishing and probing of tetheredDNA molecule in a nanopore. a) Fishing mode, with t_(fish)=0.521 sec. b)Probing mode, in which the FSM applies 150 mV until a DNA alone event isdiagnosed. In the event shown, enzyme-bound DNA is diagnosed, and theFSM continues to monitor the filtered amplitude. c) The terminal step isdiagnosed, using the [7.5, 15.5] pA threshold, and the fishing phase isrestarted. d) Fishing mode.

FIG. 19 illustrates a proposed mechanism for translocation of DNA/KFbinary complex and DNA/KF/dGTP ternary complex through a nanopore. a)Shows a typical current trace when ternary complex is present. Partsa(i), a(ii), and a(iii) illustrate the configuration of the system foreach section of the signal. b) and c) show a dwell time event plot for a14 bphp alone and the terminal step present in ternary complex events,respectively. The similarity of the dwell times in the two plotssupports the perception that the terminal step is a result of KFdissociation. d) and e) show the same as b) and c) but for a 20 bphp. f)shows a DNA only event f(i) and a DNA/KF binary event f(ii) side byside. Note the absence of the terminal step in the DNA only event whencompared to the enzyme-bound event.

FIG. 20 illustrates a representative ternary complex event under FPGAcontrol. a(i) The FPGA diagnosed an enzyme event in the detection range[17.2 pA, 22.8 pA]. a(ii) The FPGA continued to monitor the current toensure it stayed within the detection range for at least 20 msec. Eventslasting longer than 20 msec were diagnosed as a DNA/KF/dGTP ternarycomplex event. a(iii) Upon diagnosis of a ternary complex, the FPGAreversed the voltage to −50 mV for 5 ms, ejecting the complex from thepore. The 180 mV capture voltage was then restored. b) Dwell timeprobability histograms for 24±2.8 pA events with FPGA control (527 totalevents in red) and without FPGA control (155 total events in blue).

FIG. 21 illustrates regulation of 20 base pair hairpin (bphp) dwell timeusing FSM control. (I) The red current signals are low-pass filtered at5 kHz, the blue signal is a mean filtered current, and the red voltagesignal is the commanded voltage. Typical events and correspondingvoltage signals under a) constant 180 mV voltage, b) dwell timeextension control, and c) dwell time aggregation control. (II) Eventplot of DNA events, showing average amplitude vs. dwell time for eachevent. (III) Probability histograms of the base 10 logarithm of dwelltime for all events (filled bars), and for subset of events in range 13to 18 pA (open bars).

FIG. 22 illustrates repeated KF binding events using a singlepolynucleotide oligomer. a) Captured hairpin or hairpin bound with KF at180 mV. b) Hairpin was held in vestibule at 50 mV for trans-side primerto anneal (20 sec). c) Fished for KF at −20 mV for 5 sec. d) 180 mVapplied to check for presence of KF. If enzyme binding does not occur,bare DNA was immediately detected in the pore. Otherwise, the FSM waitedfor KF to dissociate, leaving hairpin in vestibule (20 pA terminalstep). In both cases, once bare DNA is present in the pore, the FSMreverses the voltage (−20 mV) before the hairpin unzips to fish foranother KF. Steps c) through d) were repeated until the hairpintranslocated.

DETAILED DESCRIPTION OF THE INVENTION

The embodiments disclosed in this document are illustrative andexemplary and are not meant to limit the invention. Other embodimentscan be utilized and structural changes can be made without departingfrom the scope of the claims of the present invention.

As used herein and in the appended claims, the singular forms “a,” “an,”and “the” include plural reference unless the context clearly dictatesotherwise. Thus, for example, a reference to “a nanaopore” includes aplurality of such nanaopores, and a reference to “a signal” is areference to one or more signals and equivalents thereof, and so forth.

By “polynucleotide” is meant DNA or RNA, including any naturallyoccurring, synthetic, or modified nucleotide. Nucleotides include, butare not limited to, ATP, dATP, CTP, dCTP, GTP, dGTP, UTP, TTP, dUTP,5-methyl-CTP, 5-methyl-dCTP, ITP, dITP, 2-amino-adenosine-TP,2-amino-deoxyadenosine-TP, 2-thiothymidine triphosphate,pyrrolo-pyrimidine triphosphate, 2-thiocytidine as well as thealphathiotriphosphates for all of the above, and2′-O-methyl-ribonucleotide triphosphates for all the above bases.Modified bases include, but are not limited to, 5-Br-UTP, 5-Br-dUTP,5-F-UTP, 5-F-dUTP, 5-propynyl dCTP, and 5-propynyl-dUTP.

By “transport property” is meant a property measurable during polymermovement with respect to a nanopore. The transport property may be, forexample, a function of the solvent, the polymer, a label on the polymer,other solutes (for example, ions), or an interaction between thenanopore and the solvent or polymer.

A “hairpin structure” is defined as an oligonucleotide having anucleotide sequence that is about 6 to about 100 nucleotides in length,the first half of which nucleotide sequence is at least partiallycomplementary to the second part thereof, thereby causing thepolynucleotide to fold onto itself, forming a secondary hairpinstructure.

A “hairpin shaped precursor” is defined as a hairpin structure that isprocessed by a Microprocessor complex and then by a Dicer enzymecomplex, yielding an oligonucleotide that is about 16 to about 24nucleotides in length.

“Identity” or “similarity” refers to sequence similarity between twopolynucleotide sequences or between two polypeptide sequences, withidentity being a more strict comparison. The phrases “percent identity”and “% identity” refer to the percentage of sequence similarity found ina comparison of two or more polynucleotide sequences or two or morepolypeptide sequences. “Sequence similarity” refers to the percentsimilarity in base pair sequence (as determined by any suitable method)between two or more polynucleotide sequences. Two or more sequences canbe anywhere from 0-100% similar, or any integer value therebetween.Identity or similarity can be determined by comparing a position in eachsequence that may be aligned for purposes of comparison. When a positionin the compared sequence is occupied by the same nucleotide base oramino acid, then the molecules are identical at that position. A degreeof similarity or identity between polynucleotide sequences is a functionof the number of identical or matching nucleotides at positions sharedby the polynucleotide sequences. A degree of identity of polypeptidesequences is a function of the number of identical amino acids atpositions shared by the polypeptide sequences. A degree of homology orsimilarity of polypeptide sequences is a function of the number of aminoacids at positions shared by the polypeptide sequences.

The term “incompatible” refers to the chemical property of a moleculewhereby two molecules or portions thereof cannot interact with oneanother, physically, chemically, or both. For example, a portion of apolymer comprising nucleotides can be incompatible with a portion of apolymer comprising nucleotides and another chemical moiety, such as forexample, a peptide nucleic acid, a 2′-O-methyl group, a fluorescentcompound, a derivatized nucleotide, a nucleotide isomer, or the like. Inanother example, a portion of a polymer comprising amino acid residuescan be incompatible with a portion of a polymer comprising amino acidresidues and another chemical moiety, such as, for example, a sulfategroup, a phosphate group, an acetyl group, a cyano group, a piperidinegroup, a fluorescent group, a sialic acid group, a mannose group, or thelike.

“Alignment” refers to a number of DNA or amino acid sequences aligned bylengthwise comparison so that components in common (such as nucleotidebases or amino acid residues) may be visually and readily identified.The fraction or percentage of components in common is related to thehomology or identity between the sequences. Alignments may be used toidentify conserved domains and relatedness within these domains. Analignment may suitably be determined by means of computer programs knownin the art, such as MACVECTOR software (1999) (Accelrys, Inc., SanDiego, Calif.).

The terms “highly stringent” or “highly stringent condition” refer toconditions that permit hybridization of DNA strands whose sequences arehighly complementary, wherein these same conditions excludehybridization of significantly mismatched DNAs. Polynucleotide sequencescapable of hybridizing under stringent conditions with thepolynucleotides of the present invention may be, for example, variantsof the disclosed polynucleotide sequences, including allelic or splicevariants, or sequences that encode orthologs or paralogs of presentlydisclosed polypeptides. Polynucleotide hybridization methods aredisclosed in detail by Kashima et al. (1985) Nature 313: 402-404, andSambrook et al. (1989) Molecular Cloning: A Laboratory Manual, 2nd Ed.,Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (“Sambrook”);and by Haymes et al., “Nucleic Acid Hybridization: A PracticalApproach”, IRL Press, Washington, D.C. (1985), which references areincorporated herein by reference.

In general, stringency is determined by the incubation temperature,ionic strength of the solution, and concentration of denaturing agents(for example, formamide) used in a hybridization and washing procedure(for a more detailed description of establishing and determiningstringency, see below). The degree to which two nucleic acids hybridizeunder various conditions of stringency is correlated with the extent oftheir similarity. Thus, similar polynucleotide sequences from a varietyof sources, such as within an organism's genome (as in the case ofparalogs) or from another organism (as in the case of orthologs) thatmay perform similar functions can be isolated on the basis of theirability to hybridize with known peptide-encoding sequences. Numerousvariations are possible in the conditions and means by whichpolynucleotide hybridization can be performed to isolate sequenceshaving similarity to sequences known in the art and are not limited tothose explicitly disclosed herein. Such an approach may be used toisolate polynucleotide sequences having various degrees of similaritywith disclosed sequences, such as, for example, sequences having 60%identity, or more preferably greater than about 70% identity, mostpreferably 72% or greater identity with disclosed sequences.

Single-channel thin film devices and methods for using the same areprovided. The subject devices comprise cis and trans chambers connectedby an electrical communication means. At the cis end of the electricalcommunication means is a horizontal conical aperture sealed with a thinfilm that includes a single nanopore or channel. The devices furtherinclude a means for applying an electric field between the cis and transchambers. The subject devices find use in applications in which theionic current through a nanopore or channel is monitored, where suchapplications include the characterization of naturally occurring ionchannels, the characterization of polymeric compounds, and the like.Current sequencing methods are limited to read-lengths of about onekilobase (1000 base pairs identified), but the invention disclosedherein has potential for much longer read-lengths when compare withtraditional bulk sequencing methods (Metzker (2005) Genome res. 15:1767-1776; Rhee and Burns (2006) TIBS 24: 580-586)

Devices that can be used to carry out the methods of the instantinvention are described in for example, U.S. Pat. Nos. 5,795,782,6,015,714, 6,267,872, 6,746,594, 6,428,959, and 6,617,113, each of whichis hereby incorporated by reference in their entirety. The invention isbest understood by the examples and methods disclosed herein.

It is now understood that a means to control the time at which enzymaticactivity begins for an individual polymer in a mixture would be anadvantage. That is, absent such a control, initiation of enzyme activity(for example by addition of Mg²⁺ cofactor to a bath containing enzymeand DNA) would begin at once and that enzyme-polynucleotide complexeswould necessarily be at many points along the target strands whencaptured by the nanopore in a time series. At least five methods can beused to overcome these potential multiple interactions:

-   -   a) Microfluidics. A factor for inducing enzyme activity may be        added only after an enzyme-polynucleotide complex is captured by        the pore. After that polynucleotide is processed, the bath can        be flushed and a new population of polynucleotide targets added        absent the inducing factor. The cycle is then repeated.    -   b) Protein engineering. By covalently linking an enzyme to a        pore, it can be possible to have only one enzyme in the system        and it will be immediately adjacent to the pore (some methods to        achieve this are articulated in U.S. application Ser. No.        10/739,585).    -   c) Block activity of enzymes in bulk phase using an agent        released only by capture of a complex in the nanopore. This is        illustrated by examples in the figures (FIGS. 1 and 2) and        described herein.

Assume a DNA primer-template pair (at about 1 μM) in a solution thatcontains all required dNTPs (at about 200 μM each), Mg²⁺ (at about 5mM), and a processive DNA polymerase (at about 1 μM). The solution is incontact with a single nanopore (for example, α-hemolysin) with anapplied voltage such that negatively charged DNA is drawn into the pore.Each primer-template pair is also annealed to a sequence specificmolecule at (or close to) the first base that will be added to theprimer strand (position n=0). This molecule may have any of numerousstructures but will likely be PNA or 2′-O-methyl substituted DNA in theearly trials. This blocking molecule either inhibits binding of thepolymerase at the initiation site (FIG. 1) or it allows binding butprevents strand synthesis (FIG. 2). The blocking molecule includes aloop that is sufficiently large that it cannot enter the nanopore. Thus,when the strand is pulled into the pore under applied voltage, this loopis hung-up at the pore orifice. This initiates unzipping of the blockfrom the primer template and the blocking primer dissociates. Polymerasebinding and polymerase-catalyzed strand synthesis can follow. The pointof this method is that only the strand captured by the nanopore isunlocked from the blocking primer at the instant it is to be examined.When optimized, a 100 μl volume containing 1 μM of DNA primer/templaterepresents one nanopore-activated molecule in 6×10′³ molecules total.

-   -   d) Deliver a cofactor through the pore from the trans-side to        the cis-side (containing enzyme). This can effectively restrict        the required factor to the volume immediately adjacent to the        pore. An example is Mg²⁺. This is illustrated by examples in the        figure (FIG. 3) and described herein.

An example of this approach is illustrated in FIG. 3. Mg²⁺ is aco-factor essential for catalytic activity by many DNA and/or RNAmodifying enzymes including polynucleotide polymerases. In thisscenario, Mg²⁺ at greater than millimolar concentrations are added tothe trans compartment. The cis compartment comprises all the otherreagents, enzymes, and substrates necessary for catalysis. The ciscompartment also comprises trace concentrations of EDTA (at about 0.1mM) to ensure that free [Mg²+] on the cis side is effectively zero inbulk phase. Since Mg²⁺ is a divalent cation under physiologicalconditions, an applied voltage that attracts a polynucleotide into thenanopore (trans side +) would drive Mg²⁺ in the opposite directiontowards the cis compartment. Thus, in the volume (area of medium)immediately adjacent to the pore aperture, the free [Mg²⁺] is a functionof the voltage-driven flux from the trans side to the cis side acrossthe nanopore minus the Mg²⁺ fraction complexed by 0.1 mM EDTA and minusthe rate of Mg²⁺ diffusion away from the volume (area of medium)adjacent to the nanopore aperture. [Mg²⁺] in the bulk volume remainseffectively zero and is dominated by EDTA complexation of divalentmetal(s).

-   -   e) Deliver ssDNA template through the pore from the trans side        to the cis side containing enzyme. This can effectively restrict        enzyme processing of the template to the molecule captured in        the pore. All other template strands are isolated from enzymes        by the impermeable layer (a bilayer for example) supporting the        channel.

Enzymes that interact with polynucleotides are known to those of skillin the art and can include, but are not limited to, DNA polymerase suchas a DNA polymerase selected from E. coli DNA polymerase I, E. coli DNApolymerase I Large Fragment (Klenow fragment), phage T7 DNA polymerase,Phi-29 DNA polymerase, Thermus aquaticus (Taq) DNA polymerase, Thermusflavus (Tfl) DNA polymerase, Thermus Thermophilus (Tth) DNA polymerase,Thermococcus litoralis (Tli) DNA polymerase, Pyrococcus furiosus (Pfu)DNA polymerase, VENT DNA polymerase, Bacillus stearothermophilus (Bst)DNA polymerase, AMV reverse transcriptase, MMLV reverse transcriptase,and HIV-1 reverse transcriptase, RNA polymerase such as RNA polymeraseselected from T7 RNA polymerase, T3 RNA polymerase, SP6 RNA polymerase,and E. coli RNA polymerase, and an exonuclease such as exonucleaseLambda, T7 Exonuclease, Exo III, RecJ₁ Exonuclease, Exo I, and Exo T.

Nanopore-Coupled Sequencing by Synthesis

This is a technique for sequencing of single DNA molecules. It combinesfeatures of conventional sequencing by synthesis (SBS) with novelnanopore analysis of single DNA molecules under electronic andbiochemical feedback control. It relies upon 3′ terminator technology,specifically reversible terminator technology.

The basic strategy is outlined in FIG. 4 for a single nanopore. Ourlaboratory has developed a strategy to perform this analysis on a chipwith up to 400,000 pores. Design and fabrication of such a chip aredisclosed below.

As illustrated in FIG. 4, A DNA molecule with both doubled-stranded andsingle-stranded segments is captured in a nanoscale pore under anapplied voltage (trans side positive) (Step a: FIG. 4). DNA of thisnature can be generated by timed exonuclease digestion of restrictionfragments from genomic DNA or from BAC clones etc. The nanopore is largeenough to permit translocation of the ssDNA segment, but thedouble-stranded segment cannot translocate because its diameter is toolarge to fit through the narrowest part of the pore. The α-hemolysinpore is ideal for this and is therefore used to illustrate thetechnique. Strand capture and entry of the duplex segment into the porevestibule can be confirmed based on current amplitude. Once this isachieved, the voltage is reduced under feedback control (Step b: FIG.4). At this point, the duplex terminus can be examined and identified byany of several techniques. For example, an earlier patent from thislaboratory demonstrated that duplex termini can be identified based onDC current impedance alone. At the same time, the 5′-end of the ssDNA onthe trans side of the channel is annealed to an agent (for example, acomplementary oligonucleotide or streptavidin) that keeps the strand inthe pore indefinitely.

Once the DNA strand is captured and the terminus identified, the ciscompartment is perfused with a buffer containing Mg²⁺, a DNA polymerase(for example, the Klenow fragment (KF) of DNA polymerase), and each ofthe four dNTPs protected with a distinct reversible terminator or by anidentical reversible terminator (Step c: FIG. 4). The membrane potentialis then reversed thus driving the duplex terminus of the target strandinto the cis compartment containing the polymerase and substrates (Stepc: FIG. 4). Sufficient time is then allowed for the correct protecteddNTP to be added to the target (Step e: FIG. 4). When that time haselapsed, the voltage is reversed once again (trans-side positive; Stepf: FIG. 4). The duplex terminus is pulled next to the pore'slimiting-aperture where the identity of the added nucleotide isestablished. If no protected nucleotide has been added, the signal willbe the same as in Step b. If this is the case, Steps d to f are repeateduntil the correct nucleotide is added and identified. Followingconfirmed addition of the protected nucleotide, the cis compartment isperfused and a deprotecting buffer is added (Step g: FIG. 4).Alternatively, we envision a scenario where a deprotecting agent locatedonly near the nanopore is activated or deactivated under our controlthat would eliminate the need for perfusion. The deprotecting agent maybe an enzyme (for example, alkaline phosphatase), light, or a solute(for example, palladium to catalyze deallylation). After perfusion, atrans-side negative potential is established, driving the duplexterminus into the cis compartment where the reversible terminator can beremoved (Step h: FIG. 4). Following this reaction, a trans-side positivepotential is re-established, drawing the duplex terminus back to thelimiting aperture where it can be examined to determine if deprotectionhas been successfully achieved, and to confirm the identity of the lastbase (Step i: FIG. 4). In the event that deprotection is not successful,steps h and i are repeated. If deprotection was successful, the cycle isrepeated at step b.

The scenario illustrated in FIG. 5 is similar to that illustrated inFIG. 4 except that exonuclease digestion takes place on the trans sideof the channel and the DNA is captured in reverse orientation comparedto FIG. 4. In this strategy, the template strand is held in place on thecis side by the primer from which strand synthesis originates. Theadvantage of this scenario is that ssDNA fed into to the nanopore can begenerated in blocks by a series of timed exonuclease digestions in thetrans compartment. Thus, most of the template would be as dsDNA. Forexample, if the exonuclease cut at 10 ms per base (on average), a 1000base overhang could be generated at the end of a 20 kb dsDNA target.When about 1000 bases were successfully filled in by nanopore-coupledSBS, the exonuclease (or a required cofactor) could be re-added to thetrans compartment and allowed to react for an additional 10 seconds. Thenewly generated ssDNA would be filled in base-by-base in the ciscompartment as before. This would be repeated in approximately tworounds of 1000 bases to complete the 20 kb fragment.

The pore aperture can vary in dimensions, for example it can have adiameter of between about 0.5 nm and 10 nm in size. For example, thediameter can be about 0.5 nm, 1 nm, 1.25 nm, 1.5 nm, 1.75 nm, 2 nm, 2.25nm, 2.5 nm, 2.75 nm, 3 nm, 3.5 nm, 4 nm, 4.5 nm, 5 nm, 6 nm, 7 nm, 8 nm,9 nm, 10 nm, or any dimension therebetween.

Nanopore-coupled sequencing by synthesis has several advantages overconventional SBS, but the main advantages are these:

-   -   1) Nucleotide addition and reversible terminator removal can be        directly measured on the individual target strand.    -   2) The system is controlled both electronically and        biochemically so that nucleotide addition and deprotection steps        can be repeated rapidly until they are successful.    -   3) A very long DNA molecule can be captured, manipulated, and        quantitatively retained in the pore for an indefinite period.    -   4) The volume of reagents that are used can be very small (on        the order of 100 μl), and it is possible that a given volume can        be recycled hundreds of times. With further development, it may        be possible to control activation and deactivation of the        deprotection step at the nanopore orifice. This would completely        eliminate the need for perfusion.

As is true with conventional SBS, this assay can be performed inparallel. We envision as many as 400,000 independently addressable poreson a 1 cm×1 cm chip that can be fabricated using conventionallithography (see separate disclosure below).

Here we propose polynucleotides that can be used to place and attachmacromolecules and other polyanions/polycations at the nanoporeaperture. Such macromolecules and polymers can be, for example, apolynucleotide-binding protein, such as, but not limited to apolynucleotide polymerase at the nanopore orifice. A nanopore has theuseful property of bringing virtually any desired macromolecularstructure to a defined site that can be specified by the user. Afterbeing placed at the nanopore site, macromolecular functions can bemonitored by the user in a variety of ways. This method can be appliedto macromolecules such as, but not limited to, enzymes, receptorproteins, ribozymes, and ribosomes. The method can be applied either tobiological pores, or to solid state pores produced in thin inorganicmembranes.

The basis of this invention is that a sufficiently long strand of anionized polymer can be attached to the desired macromolecule, either bycovalent or non-covalent bonds. The polymer is then drawn through thenanopore by an electrical voltage applied across the membrane. In someapplications, it may be necessary to regulate the force on themacromolecule by varying the voltage acting across the pore. As aresult, the macromolecule is placed at the site of the pore withsub-nanometer precision. The macromolecule is then maintained at thepore site either by the electrical force produced by the transmembranevoltage, or by a covalent bond that is engineered between themacromolecule and the pore, or the surface adjacent to the pore. Morethan one macromolecule can be attached in series if desired.

Functions of the single macromolecule can then be monitored byelectrical effects produced at the pore. For instance, the ionic currentthrough the pore can be measured and molecular functions are detected asmodulations of the current. Alternatively, an electrode such as a carbonnanotube is placed across the pore and molecular functions are detectedby modulations of the electronic current through the nanotube.

Exemplary Uses of the Invention

(1) A nanopore device can be used to monitor the turnover of enzymessuch as exonucleases and polymerases, which have important applicationsin DNA sequencing.

(2) A nanopore device can function as a biosensor to monitor theinteraction between soluble substances such as enzyme substrates orsignaling molecules. Examples include blood components such as glucose,uric acid and urea, hormones such as steroids and cytokines, andpharmaceutical agents that exert their function by binding to receptormolecules.

(3) A nanopore device can monitor in real time the function of importantbiological structures such as ribosomes, and perform this operation witha single functional unit.

FIGS. 6 through 8 illustrate exemplary embodiments of the invention.

FIG. 6

FIG. 6A illustrates a nanopore device comprising a pore aperture (1) ina substrate or structure (2) having a compound (3) bound adjacent to thepore aperture; the substrate or structure defining a cis side and atrans side. FIG. 6A further shows a molecule or macromolecule (4) boundto a polymer (5) to create a macromolecule/polymer complex, the polymerfurther comprising an incompletely synthesized portion (6).

As illustrated by FIG. 6B, a voltage gradient is applied to the deviceto draw the macromolecule/polymer complex to the cis side of thesubstrate or structure. The incompletely synthesized portion (6) hasdimensions sufficient to pass through the pore aperture. Alsoillustrated are monomers (7) present on the cis side. The change inlocation of the macromolecule/polymer complex can be measured by thechange in current (arrow; δI) across the pore aperture. Themacromolecule then incorporates the monomers into the polymer to createa completely synthesized polymer (8) as shown in FIG. 6C.

The voltage gradient is then reversed, and as illustrated in FIG. 6C,the completely synthesized polymer is released from the macromolecule,thereby further creating a change in current (δI). This may beexemplified by using a DNA polymerase as the macromolecule.

In the alternative, as illustrated in FIG. 6D, the macromolecule excisesthe incompletely synthesized portion from the polymer, thereby releasingthe incompletely synthesized portion (6) from the macromolecule/polymercomplex. The voltage gradient is then reversed and the polymer (5) isreleased from the macromolecule. These events can also be measured by achange in the current (arrow; δI). This may be exemplified by using anendonuclease enzyme as the macromolecule.

FIG. 7

FIG. 7A illustrates a nanopore device comprising a pore aperture (1) ina substrate or structure (2) having a compound (3) bound adjacent to thepore aperture; the substrate or structure defining a cis side and atrans side. FIG. 7A further shows a molecule or macromolecule (4) boundto a polymer (5) to create a macromolecule/polymer complex, themacromolecule further comprising a high affinity binding site (9) for aligand (10), FIG. 7B.

As illustrated by FIG. 7B, a voltage gradient is applied to the deviceto draw the macromolecule/polymer complex to the cis side of thesubstrate or structure. The polymer (5) is then covalently bound to thecompound (3) thereby bringing adjacent to the pore aperture (1). Thechange in location of the macromolecule/polymer complex can be measuredby the change in current (arrow; δI) across the pore aperture.

The ligand (10) is then allowed to bind to the high affinity bindingsite (9), and as illustrated in FIG. 7C, thereby further creating achange in current (arrow; δI). This may be exemplified by using asteroid hormone receptor as the macromolecule and a polyaspartic acid asthe polymer.

In the alternative, as illustrated in FIG. 7D, the macromoleculemetabolizes the ligand into two products (11), thereby releasing theproducts from the macromolecule/polymer complex. The voltage gradient isthen reversed and the products are released from the macromolecule.These events can also be measured by a change in the current (δI). Thismay be exemplified by using a glucose oxidase enzyme or a proteinphosphatase enzyme as the macromolecule.

FIG. 8

FIG. 8A illustrates a nanopore device comprising a pore aperture (1) ina substrate or structure (2) having a compound (3) bound adjacent to thepore aperture; the substrate or structure defining a cis side and atrans side. FIG. 8A further shows a molecule or macromolecule (4) boundto a first polymer (5) to create a macromolecule/polymer complex.

As illustrated by FIG. 8B, a voltage gradient is applied to the deviceto draw the macromolecule/polymer complex to the cis side of thesubstrate or structure. Also illustrated are a second polymer (12)present on the cis side and monomers (7) present on the trans side. Inthe alternative, the monomers (7) may be on the cis side (not shown).The polymer (5) is then covalently bound to the compound (3) therebybringing adjacent to the pore aperture (1). The change in location ofthe macromolecule/polymer complex can be measured by the change incurrent (arrow; δI) across the pore aperture.

As illustrated in FIG. 8C, the second polymer (12) binds to themacromolecule (4) and is drawn by the potential difference though theaperture to the trans side. As the second polymer is drawn through themacromolecule co-ordinately synthesizes a third polymer (13) using themonomers (7), thereby further creating a change in current across thepore aperture (see FIG. 8D). In the alternative, the third polymer (13)can be synthesized on the cis side (not shown). These events can also bemeasured by a change in the current (δI). This may be exemplified byusing a ribosome as the macromolecule and a messenger RNA as the firstpolymer. In an alternative, a ribosome may be used as the macromoleculeand a polyaspartic acid as the third polymer.

Manufacture of Single Channel Thin Film Devices

Single-channel thin film devices and methods for using the same areprovided. The subject devices comprise a mixed-signal semiconductorwafer, at least one electrochemical layer, the electrochemical layercomprising a semiconductor material, such as silicon dioxide or thelike, wherein the semiconductor material further comprises a surfacemodifier, such as a hydrocarbon, wherein the electrochemical layerdefines a plurality of orifices, the orifices comprising a chamber and aneck and wherein the chamber of the orifices co-localize with a firstmetal composition of the mixed-signal semiconductor wafer, wherein aportion of the orifice is plugged with a second metal, for example,silver, wherein the second metal is in electronic communication with thefirst metal, and wherein the orifice further comprises a thin film, suchas a phospholipid bilayer, the thin film forming a solvent-impermeableseal at the neck of the orifice, the thin film further comprising apore, and wherein the orifice encloses an aqueous phase and a gas phase.In a preferred embodiment the metallization layer comprises a metal, ormetal alloy, such as, but not limited to, nickel, gold, copper, andaluminum.

FIG. 9 illustrates a side cutaway perspective of the invention.

FIG. 10 illustrates an overhead perspective of the invention showingportions of four adjacent elements of the invention.

FIG. 11 illustrates a flow chart disclosing the method of using theinvention as manufactured.

Biological nanopores have utility in sequencing of polynucleotides but,due to the low current used (approximately in the tens of picoamps),detection using high-throughput of a single nanopore sequencing devicemay be limited to approximately 1000 base pairs per second.Manufacturing arrays of biological nanopores that can operateindependently of each other, such as used in the manufacture of verylarge arrays of integrated circuits, a very large scale array ofnanopores may perform millions of biochemical reactions and analyses ina single second.

The array elements may be manufactured in a step-wise parallel manner,similar to the manufacture of transistors on integrated circuits. All,or most, of the similar layers of each array element are created in asequence of single process steps that simultaneously take place on all.Or most, of the array elements.

There appears to be no simple way to synchronize the activities ofseparate molecules of biological reagents, so each element in the arrayshould be able to act independently of the other elements. This may beaccomplished by including a digital logic circuit with each singlebiological nanopore that implements a finite state machine that controlsand senses the biochemical state of the complex off single (or multiple)molecules associated with the biological nanopore. The finite statemachine allows low latency control of the complex of moleculesassociated with the biological nanopore and at the same time can storeinformation gathered for retrieval at another time.

In order that the each of the hundreds of thousands of biologicalnanopore elements may be in communication with one another using aminimum number of wired connections, a serial interface and addressablelogic can be used to multiplex the large amount of data entering andexiting the array (see flowchart on FIG. 11).

FIG. 9 illustrates a diagram of the manufactured array. An exemplarymethod of manufacture is herewith disclosed. A commercially availablemixed-signal semiconductor wafer (15) comprising the analog and digitalcircuitry that is to be used serves as the base layer. Electrochemicallayer(s) (16) may then be overlain. A metal (19), for example silver, isdeposited on exposed metallization (18) to simultaneously create all ormost of the electrodes for the nanopore system. As is well known tothose of skill in the art, oxide (2) is growth to a thickness sufficientto encapsulate a volume equal to that of a volume of liquid that willoccupy the area above the electrode. The surface of the oxide ischemically modified (16, 3) to allow wetting of the orifice and toimprove lipid bilayer (thin film, 20) seal resistance. A small amount ofgas (21), for example, nitrogen gas, is trapped in the areas adjacent tothe electrodes that are not chemically modified. The gas is trappedbecause oxide that is not chemically modified repels water (or anaqueous solution). The trapped gas (21) can be used to apply suction toany one of the bilayers (20) via removal of controlled heating from theunderlying electronic circuitry. The high thermal conductivity of themetallization and metal transfers the controlled heat from theelectronic circuitry to the trapped gas.

The lipid layer(s), including both the monolayer (22) over thechemically modified oxide and the bilayer across the orifice (17), isapplied by pressing the chemically modified wafer to a TEFLON film thathas been coated on one surface with lipid. This can occur within aliquid or aqueous solution (23) present in the chamber or well (24).Removal of the overlaying TEFLON film leaves the lipid layer(s) (20, 22)overlying a first solution (23) as shown in FIGS. 9A, 9B, and 9C.

It is of note that, following the above recited method and procedure,not all of the array elements may have a thin film or bilayer acrosstheir respective orifice. The capacitance of lipid present in theorifice as measured by the finite state machine can be used to detectthe presence of non-functional array elements. If it subsequentlydetermined that a proportion of array elements lack a thin film orbilayer is greater when compared with a proportion that is preferred,then the step of overlaying the TEFLON film and lipid coat can berepeated.

As shown in FIG. 9A, a second solution (25) that may comprise buffersthat stabilizes pH for any biochemical reagents used and supportingelectrolyte comprising between about 0.1M and about 5M KCl or othersuitable salt. Second solution (25) covers the array elements as anunbroken drop of liquid. An electrode, for example a groundedmacroscopic AgCl electrode, is placed in contact with second solution(25). When bilayers are positioned in place across all the functionableorifices, no ion current will flow from second solution (25) to firstsolution (23). A predetermined amount of pore molecule or channelmolecule (14), such as for example, α-hemolysin toxin, is added tosecond solution (25). The concentration of pore molecule or channelmolecule (14) is sufficient to form a single channel in any of the thinfilms or bilayers in approximately, for example, fifteen minutes. Thetime to form such channels can be for example, between one-half minuteand one hour, for example, about one-half minute, one minute, twominutes, three minutes, four minutes, five minutes, seven minutes, tenminutes, fifteen minutes, twenty minutes, twenty five minutes, thirtyminutes, thirty five minutes, forty minutes, forty five minutes, fiftyminutes, fifty five minutes, sixty minutes, or any time therebetween.The time for formation can be altered by an operator by several factorsor parameters, for example, increasing or decreasing the ambient orincubation temperature, increasing or decreasing the concentration ofsalt in second solution (25) or first solution (23), placing a potentialdifference between the first solution and the second solution thatattracts the pore or channel molecule towards the thin film or bilayer,or other methods know to those of skill in the art. The finite statemachine can detect and/or sense formation of a single channel in itscorresponding bilayer by reacting to the flow of current (ions) throughthe circuit, the circuit comprising the macroscopic electrode, thesecond solution, the single nanopore or channel molecule, firstsolution, and the metal (19) electrode for any given array element.

Formation of biological channels is a stochastic process. Once a singlechannel has formed in a given array element bilayer, it is preferredthat the chance that a second channel so forming therein is reduced orpreferably, eliminated. The probability of second channel insertion canbe modulated with applied potential, that is potential difference,across the bilayer. Upon sensing a single channel, the finite statemachine adjusts the potential on the metal electrode to decrease thepossibility of second channel insertion into the same bilayer.

Despite the precautions taken in the previous step(s) a second channelmay form in a given bilayer. The finite state machine can detect theformation of the second channel. A pulse of suction from the nitrogengas beneath the orifice may force one or more channels out from thebilayer. A heating element can be included proximal to the gas that isused to heat and thereby expand the gas under controlled conditions. Apulse of precisely controlled low pressure can force one out of twochannels allowing a single channel to remain embedded in the bilayer.The finite state machine can remove one or more channels from thebilayer by inactivating the heating element and that results incontraction of the gas and applies suction to the bilayer.

In the course of using the biological nanopore for biochemical actuationand detection, the pore may become permanently obstructed. The finitestate machine can detect and sense this obstructed state and can removethe blocked channel from the bilayer by inactivating the heating elementthereby applying suction (reduced pressure) upon the bilayer.

In an alternative embodiment, each array element may comprise a goldelectrode (26) surrounding the orifice. This gold electrode may serve toactivate chemical reagents using reduction or oxidation reactions andthat can act specifically at the location of a specific orifice. FIG.10, for example, illustrates a vertical view of portions of four arrayelements showing the approximate spacing and placement of some of thecomponents and elements of the invention, an orifice (17), optional goldelectrode (26), and substrate or structure (2).

The finite state machine can be created using state-of-the-artcommercially available 65 nm process technology, for example from TaiwanSemiconductor Manufacturing Company, Taiwan). A 600×600 array ofnanopores can perform 360,000 biochemical reaction and detection/sensingsteps at a rate of 1000 Hz. This may enable sequencing ofpolynucleotides, for example, to proceed at a rate of 360 million baserper second per 1 cm×1 cm die cut from the semiconductor wafer.

Exemplary means for applying an electric field between the cis- andtrans-chambers are, for example, electrodes comprising an immersed anodeand an immersed cathode, that are connected to a voltage source. Suchelectrodes can be made from, for example silver chloride, or any othercompound having similar physical and/or chemical properties.

Detection

Time-dependent transport properties of the nanopore aperture may bemeasured by any suitable technique. The transport properties may be afunction of the medium used to transport the polynucleotide, solutes(for example, ions) in the liquid, the polynucleotide (for example,chemical structure of the monomers), or labels on the polynucleotide.Exemplary transport properties include current, conductance, resistance,capacitance, charge, concentration, optical properties (for example,fluorescence and Raman scattering), and chemical structure. Desirably,the transport property is current.

Exemplary means for detecting the current between the cis and the transchambers have been described in WO 00/79257, U.S. Pat. Nos. 6,46,594,6,673 6,673,615, 6,627,067, 6,464,842, 6,362,002, 6,267,872, 6,015,714,and 5,795,782 and U.S. Publication Nos. 2004/0121525, 2003/0104428, and2003/0104428, and can include, but are not limited to, electrodesdirectly associated with the channel or pore at or near the poreaperture, electrodes placed within the cis and the trans chambers, adinsulated glass micro-electrodes. The electrodes may be capable of, butnot limited to, detecting ionic current differences across the twochambers or electron tunneling currents across the pore aperture orchannel aperture. In another embodiment, the transport property iselectron flow across the diameter of the aperture, which may bemonitored by electrodes disposed adjacent to or abutting on the nanoporecircumference. Such electrodes can be attached to an Axopatch 200Bamplifier for amplifying a signal.

Applications and/or uses of the invention disclosed herein may include,but not be limited to the following:

-   -   1. Assay of relative or absolute gene expression levels as        indicated by mRNA, rRNA. and tRNA. This includes natural,        mutated, and pathogenic nucleic acids and polynucleotides.    -   2. Assay of allelic expressions.    -   3. Haplotype assays and phasing of multiple SNPs within        chromosomes.    -   4. Assay of DNA methylation state.    -   5. Assay of mRNA alternate splicing and level of splice        variants.    -   6. Assay of RNA transport.    -   7. Assay of protein-nucleic acid complexes in mRNA, rRNA, and        DNA.    -   8. Assay of the presence of microbe or viral content in food and        environmental samples via DNA, rRNA, or mRNA.    -   9. Identification of microbe or viral content in food and        environmental samples via DNA, rRNA, or mRNA.    -   10. Identification of pathologies via DNA, rRNA, or mRNA in        plants, human, microbes, and animals.    -   11. Assay of nucleic acids in medical diagnosis.    -   12. Quantitative nuclear run off assays.    -   13. Assay of gene rearrangements at DNA and RNA levels,        including, but not limited to those found in immune responses.    -   14. Assay of gene transfer in microbes, viruses and        mitochondria.    -   15. Assay of genetic evolution.    -   16. Forensic assays.        Filtered Derivative for Adaptive Terminal Step Detection Using a        Finite-State Machine

Constant voltage experiments with DNA alone and with DNA, Klenowfragment (KF) of DNA polymerase, and complementary dNTP, may be used todetermine the thresholds used for detecting the terminal step, that is,dissociation of KF/dNTP from DNA. A filtered derivative of the ioniccurrent amplitude, in addition to the filtered amplitude, may be used todetect the terminal step. In practice, the filtered amplitude isthresholded as disclosed herein, and the filtered derivative ismonitored for deflections above a set threshold. Preliminary analysisusing the exponentially weighted mean filter has shown that the filteredderivative, applied to the filtered amplitude, deflects by an order ofmagnitude in the presence of the terminal step. Experiments using boththe filtered amplitude and filtered derivative are conducted, tuning thederivative filter and deflection threshold to ensure robust detection ofKF dissociation.

Deflections of the derivative may be monitored for terminal step-leveldeflections, in principle, for any applied voltage in real time using acommon (minimum) deflection threshold. In this approach, terminal stepdetection using only the filtered derivative, and not thresholding ofthe filtered amplitude is tested. Robust detection using only thefiltered derivative may increase the range of voltages that can be usedto probe the DNA for KF binding, without requiring identification offiltered current amplitude ranges for each probing voltage. In additionto monitoring the filtered derivative for deflections, logic thatmonitors the filtered amplitude for relative amplitude changes, withoutusing preset thresholds is developed. The goal is a more adaptive ioniccurrent filtering logic that can robustly detect KF dissociation for abroad range of (possibly varying) probing voltages, using the filteredamplitude and/or filtered derivative, without dependence on presentamplitude thresholds.

Polynucleotides homologous to other polynucleotides may be identified byhybridization to each other under stringent or under highly stringentconditions. Single-stranded polynucleotides hybridize when theyassociate based on a variety of well characterized physical-chemicalforces, such as hydrogen bonding, solvent exclusion, base stacking andthe like. The stringency of a hybridization reflects the degree ofsequence identity of the nucleic acids involved, such that the higherthe stringency, the more similar are the two polynucleotide strands.Stringency is influenced by a variety of factors, including temperature,salt concentration and composition, organic and non-organic additives,solvents, etc. present in both the hybridization and wash solutions andincubations (and number thereof), as described in more detail in thereferences cited above.

Stability of DNA duplexes is affected by such factors as basecomposition, length, and degree of base pair mismatch. Hybridizationconditions may be adjusted to allow DNAs of different sequencerelatedness to hybridize. The melting temperature (T_(m)) is defined asthe temperature when 50% of the duplex molecules have dissociated intotheir constituent single strands. The melting temperature of a perfectlymatched duplex, where the hybridization buffer contains formamide as adenaturing agent, may be estimated by the following equations:DNA-DNA: T_(m)(° C.)=81.5+16.6(log [Na⁺])+0.41(% G+C)−0.62(%formamide)−500/L  (I)DNA-RNA: T_(m)(° C.)=79.8+18.5(log [Na⁺])+0.58(% G+C)+−0.12(%G+C)²−0.5(% formamide)−820/L  (II)RNA-RNA: T_(m)(° C.)=79.8+18.5(log [Na⁺])+0.58(% G+C)+0.12(%G+C)²−0.35(% formamide)−820/L  (III)where L is the length of the duplex formed, [Na⁺] is the molarconcentration of the sodium ion in the hybridization or washingsolution, and % G+C is the percentage of (guanine+cytosine) bases in thehybrid. For imperfectly matched hybrids, approximately 1° C. is requiredto reduce the melting temperature for each 1% mismatch.

Hybridization experiments are generally conducted in a buffer of pHbetween pH 6.8 to 7.4, although the rate of hybridization is nearlyindependent of pH at ionic strengths likely to be used in thehybridization buffer (Anderson and Young (1985) “Quantitative FilterHybridisation.” In: Hames and Higgins, editors, Nucleic AcidHybridisation. A Practical Approach. Oxford, IRL Press, 73-111). Inaddition, one or more of the following may be used to reducenon-specific hybridization: sonicated salmon sperm DNA or anothernon-complementary DNA, bovine serum albumin, sodium pyrophosphate,sodium dodecylsulfate (SDS), polyvinyl-pyrrolidone, ficoll, andDenhardt's solution. Dextran sulfate and polyethylene glycol 6000 act toexclude DNA from solution, thus raising the effective probe DNAconcentration and the hybridization signal within a given unit of time.In some instances, conditions of even greater stringency may bedesirable or required to reduce non-specific and/or backgroundhybridization. These conditions may be created with the use of highertemperature, lower ionic strength and higher concentration of adenaturing agent such as formamide.

Stringency conditions can be adjusted to screen for moderately similarfragments such as homologous sequences from distantly related organisms,or to highly similar fragments such as genes that duplicate functionalenzymes from closely related organisms. The stringency can be adjustedeither during the hybridization step or in the post-hybridizationwashes. Salt (for example, NaCl) concentration, formamide concentration,hybridization temperature and probe lengths are variables that can beused to alter stringency (as described by the formula above). As ageneral guidelines high stringency is typically performed at T_(m) −5°C. to T_(m) −20° C., moderate stringency at T_(m) −20° C. to T_(m) −35°C. and low stringency at T_(m) −35° C. to T_(m) −50° C. for duplex >150base pairs. Hybridization may be performed at low to moderate stringency(25-50° C. below T_(m)), followed by post-hybridization washes atincreasing stringencies. Maximum rates of hybridization in solution aredetermined empirically to occur at T_(m) −25° C. for DNA-DNA duplex andT_(m) −15° C. for RNA-DNA duplex. Optionally, the degree of dissociationmay be assessed after each wash step to determine the need forsubsequent, higher stringency wash steps.

High stringency conditions may be used to select for polynucleotidesequences with high degrees of identity to the disclosed sequences. Anexample of stringent hybridization conditions obtained in a filter-basedmethod such as a Southern or northern blot for hybridization ofcomplementary nucleic acids that have more than 100 complementaryresidues is about 5° C. to 20° C. lower than the thermal melting point(T_(m)) for the specific sequence at a defined ionic strength and pH.Conditions used for hybridization may include about 0.02 M to about 0.15M sodium chloride, about 0.5% to about 5% casein, about 0.02% SDS orabout 0.1% N-laurylsarcosine, about 0.001 M to about 0.03 M sodiumcitrate, at hybridization temperatures between about 50° C. and about70° C. More preferably, high stringency conditions are about 0.02 Msodium chloride, about 0.5% casein, about 0.02% SDS, about 0.001 Msodium citrate, at a temperature of about 50° C. polynucleotidemolecules that hybridize under stringent conditions will typicallyhybridize to a probe based on either the entire DNA molecule or selectedportions, for example, to a unique subsequence, of the DNA.

Stringent salt concentration will ordinarily be less than about 750 mMNaCl and 75 mM trisodium citrate. Increasingly stringent conditions maybe obtained with less than about 500 mM NaCl and 50 mM trisodiumcitrate, to even greater stringency with less than about 250 mM NaCl and25 mM trisodium citrate. Low stringency hybridization can be obtained inthe absence of organic solvent, for example, formamide, whereas highstringency hybridization may be obtained in the presence of at leastabout 35% formamide, and more preferably at least about 50% formamide.Stringent temperature conditions will ordinarily include temperatures ofat least about 30° C., more preferably of at least about 37° C., andmost preferably of at least about 42° C. with formamide present. Varyingadditional parameters, such as hybridization time, the concentration ofdetergent, for example, sodium dodecyl sulfate (SDS) and ionic strength,are well known to those skilled in the art. Various levels of stringencyare accomplished by combining these various conditions as needed.

The washing steps that follow hybridization may also vary in stringency;the post-hybridization wash steps primarily determine hybridizationspecificity, with the most critical factors being temperature and theionic strength of the final wash solution. Wash stringency can beincreased by decreasing salt concentration or by increasing the washtemperature. Stringent salt concentration for the wash steps willpreferably be less than about 30 mM NaCl and 3 mM trisodium citrate, andmost preferably less than about 15 mM NaCl and 1.5 mM trisodium citrate.

Thus, hybridization and wash conditions that may be used to bind andremove polynucleotides with less than the desired homology to thepolynucleotide sequences or their complements that encode the presenttranscription factors include, for example:

-   -   6×SSC at 65° C.;    -   50% formamide, 4×SSC at 42° C.; or    -   0.5×SSC, 0.1% SDS at 65° C.;        with, for example, two wash steps of 10-30 minutes each. Useful        variations on these conditions will be readily apparent to those        skilled in the art.

A person of skill in the art would not expect substantial variationamong polynucleotide species encompassed within the scope of the presentinvention because the highly stringent conditions set forth in the aboveformulae yield structurally similar polynucleotides.

If desired, one may employ wash steps of even greater stringency,including about 0.2×SSC, 0.1% SDS at 65° C. and washing twice, each washstep being about 30 min, or about 0.1×SSC, 0.1% SDS at 65° C. andwashing twice for 30 min. The temperature for the wash solutions willordinarily be at least about 25° C., and for greater stringency at leastabout 42° C. Hybridization stringency may be increased further by usingthe same conditions as in the hybridization steps, with the washtemperature raised about 3° C. to about 5° C., and stringency may beincreased even further by using the same conditions except the washtemperature is raised about 6° C. to about 9° C. For identification ofless closely related homologs, wash steps may be performed at a lowertemperature, for example, 50° C.

An example of a low stringency wash step employs a solution andconditions of at least 25° C. in 30 mM NaCl, 3 mM trisodium citrate, and0.1% SDS over 30 min. Greater stringency may be obtained at 42° C. in 15mM NaCl, with 1.5 mM trisodium citrate, and 0.1% SDS over 30 min. Evenhigher stringency wash conditions are obtained at 65° C. to 68° C. in asolution of 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Washprocedures will generally employ at least two final wash steps.Additional variations on these conditions will be readily apparent tothose skilled in the art (for example, in US Patent Application No.20010010913).

Stringency conditions can be selected such that an oligonucleotide thatis perfectly complementary to the coding oligonucleotide hybridizes tothe coding oligonucleotide with at least about a 5-10× higher signal tonoise ratio than the ratio for hybridization of the perfectlycomplementary oligonucleotide to a polynucleotide encoding atranscription factor known as of the filing date of the application. Itmay be desirable to select conditions for a particular assay such that ahigher signal to noise ratio, that is, about 15× or more, is obtained.Accordingly, a subject polynucleotide will hybridize to a unique codingoligonucleotide with at least a 2× or greater signal to noise ratio ascompared to hybridization of the coding oligonucleotide to apolynucleotide encoding known polypeptide. The particular signal willdepend on the label used in the relevant assay, for example, afluorescent label, a colorimetric label, a radioactive label, or thelike. Labeled hybridization or PCR probes for detecting relatedpolynucleotide sequences may be produced by oligolabeling, nicktranslation, end-labeling, or PCR amplification using a labelednucleotide.

Encompassed by the invention are polynucleotide sequences that arecapable of hybridizing to polynucleotides and fragments thereof undervarious conditions of stringency (for example, in Wahl and Berger (1987)Methods Enzymol. 152: 399-407, and Kimmel (1987) Methods Enzymol. 152:507-511). Estimates of homology are provided by either DNA-DNA orDNA-RNA hybridization under conditions of stringency as is wellunderstood by those skilled in the art (Hames and Higgins, Editors(1985) Nucleic Acid Hybridisation: A Practical Approach, IRL Press,Oxford, U.K.). Stringency conditions can be adjusted to screen formoderately similar fragments, such as homologous sequences fromdistantly related organisms, to highly similar fragments, such as genesthat duplicate functional enzymes from closely related organisms.Post-hybridization washes determine stringency conditions.

Characterization and Uses of the Invention

Sequencing

In one embodiment, the invention may be used to perform sequenceanalysis of polynucleotides. The analyses have an advantage over theprior art and the current art in that a single analysis may be performedat a single site, thereby resulting in considerable cost savings forreagents, substrates, reporter molecules, and the like. Of additionalimport is the rapidity of the sequencing reaction and the signalgenerated, thereby resulting in an improvement over the prior art.

Other methods for sequencing nucleic acids are well known in the art andmay be used to practice any of the embodiments of the invention. Thesemethods employ enzymes such as the Klenow fragment of DNA polymerase I,SEQUENASE, Taq DNA polymerase and thermostable T7 DNA polymerase(Amersham Pharmacia Biotech, Piscataway N.J.), or combinations ofpolymerases and proofreading exonucleases such as those found in theELONGASE amplification system (Life Technologies, Gaithersburg Md.).Preferably, sequence preparation is automated with machines such as theHYDRA microdispenser (Robbins Scientific, Sunnyvale Calif.), MICROLAB2200 system (Hamilton, Reno Nev.), and the DNA ENGINE thermal cycler(PTC200; MJ Research, Watertown Mass.). Machines used for sequencinginclude the ABI PRISM 3700, 377 or 373 DNA sequencing systems (PEBiosystems), the MEGABACE 1000 DNA sequencing system (Amersham PharmaciaBiotech), and the like. The sequences may be analyzed using a variety ofalgorithms that are well known in the art and described in Ausubel etal. (1997; Short Protocols in Molecular Biology, John Wiley & Sons, NewYork N.Y., unit 7.7) and Meyers (1995; Molecular Biology andBiotechnology, Wiley VCH, New York N.Y., pp. 856-853).

Shotgun sequencing is used to generate more sequence from cloned insertsderived from multiple sources. Shotgun sequencing methods are well knownin the art and use thermostable DNA polymerases, heat-labile DNApolymerases, and primers chosen from representative regions flanking thepolynucleotide molecules of interest. Incomplete assembled sequences areinspected for identity using various algorithms or programs such asCONSED (Gordon (1998) Genome Res. 8: 195-202) that are well known in theart. Contaminating sequences including vector or chimeric sequences ordeleted sequences can be removed or restored, respectively, organizingthe incomplete assembled sequences into finished sequences.

Extension of a Polynucleotide Sequence

The sequences of the invention may be extended using various PCR-basedmethods known in the art. For example, the XL-PCR kit (PE Biosystems),nested primers, and commercially available cDNA or genomic DNA librariesmay be used to extend the polynucleotide sequence. For all PCR-basedmethods, primers may be designed using commercially available software,such as OLIGO 4.06 primer analysis software (National Biosciences,Plymouth Minn.) to be about 22 to 30 nucleotides in length, to have a GCcontent of about 50% or more, and to anneal to a target molecule attemperatures from about 55° C. to about 68° C. When extending a sequenceto recover regulatory elements, it is preferable to use genomic, ratherthan cDNA libraries.

Use of Polynucleotides with the Invention

Hybridization

Polynucleotides and fragments thereof can be used in hybridizationtechnologies for various purposes. A probe may be designed or derivedfrom unique regions such as the 5′ regulatory region or from a conservedmotif such as a receptor signature and used in protocols to identifynaturally occurring molecules encoding the polynucleotide protein,allelic variants, or related molecules. The probe may be DNA or RNA, isusually single stranded and should have at least 50% sequence identityto any of the polynucleotide sequences. Hybridization probes may beproduced using oligolabeling, nick translation, end-labeling, or PCRamplification in the presence of labeled nucleotide. A vector containingthe polynucleotide or a fragment thereof may be used to produce an mRNAprobe in vitro by addition of an RNA polymerase and labeled nucleotides.These procedures may be conducted using commercially available kits suchas those provided by Amersham Pharmacia Biotech.

The stringency of hybridization is determined by G+C content of theprobe, salt concentration, and temperature. In particular, stringencycan be increased by reducing the concentration of salt or raising thehybridization temperature. In solutions used for some membrane basedhybridizations, addition of an organic solvent such as formamide allowsthe reaction to occur at a lower temperature. Hybridization can beperformed at low stringency with buffers, such as 5×SSC with 1% sodiumdodecyl sulfate (SDS) at 60° C., which permits the formation of ahybridization complex between polynucleotide sequences that contain somemismatches. Subsequent washes are performed at higher stringency withbuffers such as 0.2×SSC with 0.1% SDS at either 45° C. (mediumstringency) or 68° C. (high stringency). At high stringency,hybridization complexes will remain stable only where thepolynucleotides are completely complementary. In some membrane-basedhybridizations, preferably 35%, or most preferably 50%, formamide can beadded to the hybridization solution to reduce the temperature at whichhybridization is performed, and background signals can be reduced by theuse of other detergents such as Sarkosyl or Triton X-100 and a blockingagent such as denatured salmon sperm DNA. Selection of components andconditions for hybridization are well known to those skilled in the artand are reviewed in Ausubel (supra) and Sambrook et al. ((1989)Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Press,Plainview N.Y.).

Microarrays may be prepared and analyzed using methods known in the art.Oligonucleotides may be used as either probes or targets in amicroarray. The microarray can be used to monitor the expression levelof large numbers of genes simultaneously and to identify geneticvariants, mutations, and single nucleotide polymorphisms. Suchinformation may be used to determine gene function; to understand thegenetic basis of a condition, disease, or disorder; to diagnose acondition, disease, or disorder; and to develop and monitor theactivities of therapeutic agents. (See, for example, Brennan et al.(1995) U.S. Pat. No. 5,474,796; Schena et al. (1996) Proc. Natl. Acad.Sci. 93:10614-10619; Baldeschweiler et al. (1995) PCT applicationWO95/251116; Shalon et al. (1995) PCT application WO95/35505; Heller etal. (1997) Proc. Natl. Acad. Sci. 94:2150-2155; and Heller et al. (1997)U.S. Pat. No. 5,605,662.)

Hybridization probes are also useful in mapping the naturally occurringgenomic sequence. The probes may be hybridized to: (a) a particularchromosome, (b) a specific region of a chromosome, or (c) artificialchromosome construction such as human artificial chromosome (HAC), yeastartificial chromosome (YAC), bacterial artificial chromosome (BAC),bacterial P1 construction, or single chromosome cDNA libraries.

Labeling of Molecules for Assay

A wide variety of labels and conjugation techniques are known by thoseskilled in the art and may be used in various nucleic acid, amino acid,and antibody assays. Synthesis of labeled molecules may be achievedusing Promega (Madison Wis.) or Amersham Pharmacia Biotech kits forincorporation of a labeled nucleotide such as ³²P-dCTP, Cy3-dCTP orCy5-dCTP or amino acid such as ³⁵S-methionine. Nucleotides and aminoacids may be directly labeled with a variety of substances includingfluorescent, chemiluminescent, or chromogenic agents, and the like, bychemical conjugation to amines, thiols and other groups present in themolecules using reagents such as BIODIPY or FITC (Molecular Probes,Eugene Oreg.).

Feedback Control of Single Tethered Polymers to Repeatedly ProbePolymer-Binding Macromolecules

This section explains the basic mechanisms of Klenow Fragment (KF)polymerase and how dissociation of KF from its DNA template can bedetected by monitoring the pore current amplitude and event dwell times.Furthermore, the identity of the next base to be added by KF can befound through the presence of long dwell time events (such as, forexample, but not limited to >20 msec). The long dwell time events canthen be detected and reacted to using dynamic voltage control using afinite state machine (FSM).

It has been shown that KF bound to a DNA hairpin captured in a nanoporecan be differentiated from DNA hairpin alone based on current amplitude.Also, the identity the next base to be added the to a DNA hairpin can beidentified based on event dwell time. The ability to detect and react todifferent DNA/enzyme configurations and identify the base beingcatalyzed by KF is a strong motivator for the control of enzyme functionand development of a nanopore-based sequencing method, though furtherdetection and control precision is necessary.

The automated detection and control of single DNA hairpin moleculesusing the nanopore system is now described. Precise control of singleDNA molecules is necessary to make multiple sequential baseidentifications as would be employed in nanopore-based sequencing. DNAhairpin events are detected and it is shown that their dwell time can beregulated. The results presented demonstrate the level of controlnecessary for regulation of repeated enzyme binding events with a singlepiece of DNA captured in a nanopore.

It has been shown that individual DNA hairpins can be detected andcontrolled based on the amplitude of the nanpore current signal. The DNAhairpin's dwell time can be extended by reducing the applied voltageupon detection of a hairpin in the pore. Longer dwell times provide moresignal that can be used to identify the terminal base pair of thehairpin using machine learning methods (See for example, Vercoutere, etal. (2001) Nat. Biotechnol, 19(3): 248-252; and Akeson (2003) Nucleicacids research, 31: 1311-1318). An extension of the control demonstratedhere allows for the use of a single DNA hairpin to capture multipleenzymes, as shown in the next chapter.

In Examples XX through XXX, the repeated capture of enzymes with asingle DNA hairpin is demonstrated. Multiple enzyme experiments can beperformed rapidly, offering higher throughput compared to atomic forcespectroscopy (AFM) and optical tweezer methods, which require manualattachment to the molecules to be measured (See Elio et al. (2005)Nature, 438(7067): 460-465; and Greenleaf and Block (2006) Science,313(5788): 801). The ability to rapidly probe DNA/enzyme interactionsprovides further motivation for nanopore-based sequencing.

Basic detection and control of a single DNA hairpin for repeated captureof KF has been demonstrated. Real time detection of enzyme dissociationcan be made by recognizing the terminal step present in the nanoporecurrent signal of binary and ternary complex translocation events.Repeatedly probing an enzyme using a single piece of DNA achieves themechanical action necessary for quick reading of long sequences of DNAusing a nanopore. More work needs to be done to regulate single baseadditions by KF, which is also necessary for sequencing using ananopore. The terminal step detection methods presented here offersatisfactory results, but fewer false detects are necessary forsequencing using enzyme fishing to be practical.

Improvements to the enzyme fishing mechanism have been proposed. Theexponentially weighted moving average filter replace the moving averagefilter used previously to reduce computational complexity and improvesignal smoothing. An enzyme dissociation check that can confirm fishingis performed with a bare DNA hairpin to ensure each detected enzymeevent is a new enzyme binding event. This is important for use ofstatistical models for sequencing because models assume new enzymebinding events. Higher signal-to-noise can be achieved through use of alonger DNA hairpins that would allow the use of higher control voltages.Reliable detection and reaction to DNA/enzyme unbinding will allow foraccurate base identification from repeated enzyme event data.

Diagnostics

The polynucleotides, fragments, oligonucleotides, complementary RNA andDNA molecules, and PNAs may be used to detect and quantify altered geneexpression, absence/presence versus excess, expression of mRNAs or tomonitor mRNA levels during therapeutic intervention. Conditions,diseases or disorders associated with altered expression includeidiopathic pulmonary arterial hypertension, secondary pulmonaryhypertension, a cell proliferative disorder, particularly anaplasticoligodendroglioma, astrocytoma, oligoastrocytoma, glioblastoma,meningioma, ganglioneuroma, neuronal neoplasm, multiple sclerosis,Huntington's disease, breast adenocarcinoma, prostate adenocarcinoma,stomach adenocarcinoma, metastasizing neuroendocrine carcinoma,nonproliferative fibrocystic and proliferative fibrocystic breastdisease, gallbladder cholecystitis and cholelithiasis, osteoarthritis,and rheumatoid arthritis; acquired immunodeficiency syndrome (AIDS),Addison's disease, adult respiratory distress syndrome, allergies,ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis,autoimmune hemolytic anemia, autoimmune thyroiditis, benign prostatichyperplasia, bronchitis, Chediak-Higashi syndrome, cholecystitis,Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus,emphysema, erythroblastosis fetalis, erythema nodosum, atrophicgastritis, glomerulonephritis, Goodpasture's syndrome, gout, chronicgranulomatous diseases, Graves' disease, Hashimoto's thyroiditis,hypereosinophilia, irritable bowel syndrome, multiple sclerosis,myasthenia gravis, myocardial or pericardial inflammation,osteoarthritis, osteoporosis, pancreatitis, polycystic ovary syndrome,polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis,scleroderma, severe combined immunodeficiency disease (SCID), Sjogren'ssyndrome, systemic anaphylaxis, systemic lupus erythematosus, systemicsclerosis, thrombocytopenic purpura, ulcerative colitis, uveitis, Wernersyndrome, hemodialysis, extracorporeal circulation, viral, bacterial,fungal, parasitic, protozoal, and helminthic infection; a disorder ofprolactin production, infertility, including tubal disease, ovulatorydefects, and endometriosis, a disruption of the estrous cycle, adisruption of the menstrual cycle, polycystic ovary syndrome, ovarianhyperstimulation syndrome, an endometrial or ovarian tumor, a uterinefibroid, autoimmune disorders, an ectopic pregnancy, and teratogenesis;cancer of the breast, fibrocystic breast disease, and galactorrhea; adisruption of spermatogenesis, abnormal sperm physiology, benignprostatic hyperplasia, prostatitis, Peyronie's disease, impotence,gynecomastia; actinic keratosis, arteriosclerosis, bursitis, cirrhosis,hepatitis, mixed connective tissue disease (MCTD), myelofibrosis,paroxysmal nocturnal hemoglobinuria, polycythemia vera, primarythrombocythemia, complications of cancer, cancers includingadenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma,teratocarcinoma, and, in particular, cancers of the adrenal gland,bladder, bone, bone marrow, brain, breast, cervix, gall bladder,ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle,ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin,spleen, testis, thymus, thyroid, and uterus. In another aspect, thepolynucleotide of the invention.

The polynucleotides, fragments, oligonucleotides, complementary RNA andDNA molecules, and PNAs, or fragments thereof, may be used to detect andquantify altered gene expression; absence, presence, or excessexpression of mRNAs; or to monitor mRNA levels during therapeuticintervention. Disorders associated with altered expression includeakathesia, Alzheimer's disease, amnesia, amyotrophic lateral sclerosis,ataxias, bipolar disorder, catatonia, cerebral palsy, cerebrovasculardisease Creutzfeldt-Jakob disease, dementia, depression, Down'ssyndrome, tardive dyskinesia, dystonias, epilepsy, Huntington's disease,multiple sclerosis, muscular dystrophy, neuralgias, neurofibromatosis,neuropathies, Parkinson's disease, Pick's disease, retinitis pigmentosa,schizophrenia, seasonal affective disorder, senile dementia, stroke,Tourette's syndrome and cancers including adenocarcinomas, melanomas,and teratocarcinomas, particularly of the brain. These cDNAs can also beutilized as markers of treatment efficacy against the diseases notedabove and other brain disorders, conditions, and diseases over a periodranging from several days to months. The diagnostic assay may usehybridization or amplification technology to compare gene expression ina biological sample from a patient to standard samples in order todetect altered gene expression. Qualitative or quantitative methods forthis comparison are well known in the art.

The diagnostic assay may use hybridization or amplification technologyto compare gene expression in a biological sample from a patient tostandard samples in order to detect altered gene expression. Qualitativeor quantitative methods for this comparison are well known in the art.

For example, the polynucleotide or probe may be labeled by standardmethods and added to a biological sample from a patient under conditionsfor the formation of hybridization complexes. After an incubationperiod, the sample is washed and the amount of label (or signal)associated with hybridization complexes, is quantified and compared witha standard value. If the amount of label in the patient sample issignificantly altered in comparison to the standard value, then thepresence of the associated condition, disease or disorder is indicated.

In order to provide a basis for the diagnosis of a condition, disease ordisorder associated with gene expression, a normal or standardexpression profile is established. This may be accomplished by combininga biological sample taken from normal subjects, either animal or human,with a probe under conditions for hybridization or amplification.Standard hybridization may be quantified by comparing the valuesobtained using normal subjects with values from an experiment in which aknown amount of a substantially purified target sequence is used.Standard values obtained in this manner may be compared with valuesobtained from samples from patients who are symptomatic for a particularcondition, disease, or disorder. Deviation from standard values towardthose associated with a particular condition is used to diagnose thatcondition.

Such assays may also be used to evaluate the efficacy of a particulartherapeutic treatment regimen in animal studies and in clinical trial orto monitor the treatment of an individual patient. Once the presence ofa condition is established and a treatment protocol is initiated,diagnostic assays may be repeated on a regular basis to determine if thelevel of expression in the patient begins to approximate the level thatis observed in a normal subject. The results obtained from successiveassays may be used to show the efficacy of treatment over a periodranging from several days to months.

Purification of Ligand

The polynucleotide or a fragment thereof may be used to purify a ligandfrom a sample. A method for using a polynucleotide or a fragment thereofto purify a ligand would involve combining the polynucleotide or afragment thereof with a sample under conditions to allow specificbinding, detecting specific binding, recovering the bound protein, andusing an appropriate agent to separate the polynucleotide from thepurified ligand.

In additional embodiments, the polynucleotides may be used in anymolecular biology techniques that have yet to be developed, provided thenew techniques rely on properties of polynucleotides that are currentlyknown, including, but not limited to, such properties as the tripletgenetic code and specific base pair interactions.

REFERENCE NUMERALS

1. Pore or pore aperture

2. Substrate or structure

3. Compound

4. Macromolecule

5. First polymer

6. Incompletely synthesized portion of polymer

7. Monomer

8. Substantially completely synthesized polymer

9. High affinity binding site

10. Ligand

11. Product

12. Second polymer

13. Third monomer

14. Pore molecule or channel molecule

15. Mixed-signal wafer

16. Electrochemical layer

17. Orifice

18. Metallization composition

19. Metal

20. Thin film or lipid bilayer

21. Trapped gas (for example, nitrogen)

22. Lipid monolayer

23. Liquid or aqueous solution (first)

24. Chamber or well

25. Liquid or aqueous solution (second)

26. Gold electrode (optional)

To our knowledge, we are the first researchers to use an FPGA to controland measure complexes in a nanopore. (See Hornblower et al. (2007)Nature Meth. 4: 315-317.) We believe that similar functionality could beachieved with an appropriate microprocessor. FSM logic has been used aspart of a machine learning approach used to identify the terminal basepair of the blunt end of DNA hairpins (see Vercoutere, et al. (2001)Nat. Biotechnol, 19(3): 248-252; Winters-Hilt et al. (2003) Biophys. J.,84(2): 967-976). This is a much different application of an FSM in whichits primary role was for training the machine learning models offline;our FSM functionality is used for online voltage control.

Direct control of ssDNA in a nanopore (no enzymes) has been demonstrated(Bates et al (2003) Biophysical Journal, 84: 2366-2372) in whichdetection of DNA is based on monitoring the raw amplitude relative to athreshold level. Voltage level changes, comparable to those employed inWilson et al. ((2008) ibid), were commanded to explore the zero and lowvoltage e_ects on ssDNA-pore interactions. In contrast to thresholdingthe raw ionic current amplitude, our approach filters the current inreal time (details given in the Examples).

Alternative methods for single-molecule sensing and manipulation includeoptical tweezers and atomic force microscopy (see Bustamante et al.(2003) Nature, 421: 423-427). For example, optical trapping has beenused to sequence DNA by attaching a processive enzyme to a polystyrenebead (see Abbondanzieri et al (2005) Nature, 438(24):460-465; andGreenleaf and Block (2006) Science, 313:801). At present, greaterspatial and temporal resolution of single DNA molecule polymerizationhas been achieved than with nanopores. However, these methods generallyrequire more preparative steps, and far fewer molecules can be analyzedover a common time period.

Our invention uses feedback control of a single tethered DNA moleculesuspended in a nanopore for repeated capture and subsequent dissociationof individual DNA-binding enzymes. There are two phases to ourimplementation.

First, a single DNA molecule with single and double stranded segments iscaptured, by the single-stranded end, and then tethered, by making thesingle-stranded segment double-stranded on the trans side. In thisconfiguration, with double-stranded segments on both cis and trans sidesof the channel, the DNA will remain in the channel until a sufficientvoltage force unzips the double-stranded segments from the cis or transside. The length of the single-stranded segment in the channel is chosensuch that, under negative voltages, exposure of the single-to-doublestranded (ss-ds) junction in the cis chamber is sufficiently availablefor KF binding.

In the second phase, the tethered DNA is used for repeated capture anddissociation of KF enzymes in the cis chamber of the nanopore. Byanalogy with fishing, the DNA is the line and bait (with the ss-dsjunction as the hook), and the enzymes are the fish (which can be caughtonly one at a time). Details are now given on our setup, control logic,related approaches in the literature, and our initial demonstration ofrepeated KF binding to a tethered DNA molecule in a nanopore.

Impact and Refinement of Tethered DNA Capability

For the purpose of exploring the interaction of enzymes that bind ormodify DNA or RNA (exonucleases, kinases, and other polymerases), withDNA or RNA captured in a nanopore, we consider that the inventiondisclosed herein will have the following technological impacts:

-   -   Substantial increase in data throughput. In the tethered        configuration, a negative voltage is used in fishing mode, and a        positive voltage is used for probing mode. In probing mode, all        information contained in the ionic current can be used for        characterization of the polymer alone or polymer-enzyme        interactions, at any desired probing voltage. In non-tethered        configuration, independent events (including capture, blockage        of nanopore, and eventual translocation of polymer) contain the        information relevant for analysis of polymer alone or        polymer-enzyme interactions. A sufficient voltage is required        for capture of each molecule, the time between events is not        controllable, and lower capture voltages increase the time        between events. Thus, the tethered configuration increases the        throughput of analyzable data, by increasing the number of        analyzable events over a common period and by increasing the        range of probing voltages.    -   Reduction in non-analyzable data. In probing mode, the ionic        current contains information about the tethered polymer alone or        the interaction of an enzyme bound to the tethered polymer. In        non-tethered configuration, up to 50% of events recorded within        an experiment can be unrelated to the kinetics of interest. For        example, brief blockades caused by the ds-end of a DNA hairpin        contacting the cis-side of the pore would be included in data in        the non-tethered configuration, but not in the tethered        configuration.    -   Substantial increase in sensitivity of nanopore sensor for        real-time detection of the addition of biological components in        cis chamber. Post-experiment analysis demonstrates the        sensitivity of nanopore sensors for detection of the presence of        Mg²⁺ cofactor and complementary dNTP of KF. In both cases,        detection is based on the increase in dwell time for the        KF-bound portion of binary/ternary events. By monitoring the        dwell time of KF-bound portions of events in real time, the        tethered configuration offers a new capability for online        detection of addition of Mg²⁺ and complementary dNTP components        to the cis-chamber. The same capability can be utilized with        other enzymes and their corresponding event-sensitive        components. In our future tethered DNA experiments with KF,        real-time detection capabilities will be explored as a function        of fishing time, dNTP concentration, Mg²⁺ concentration, and        probing voltage.

The invention will be more readily understood by reference to thefollowing examples, which are included merely for purposes ofillustration of certain aspects and embodiments of the present inventionand not as limitations.

EXAMPLES

Herein are described several examples to demonstrate the capability ofmeasuring macromolecules and polanions or polycations.

Example I Enzyme Binding is Prevented by a Blocking Primer

For an illustration of this method, see FIGS. 1( a) through 1(g). (a) Inthis scenario, the blocking primer is bound to the primer/template inbulk phase. Structure of the ternary complex prevents binding of theenzyme to the junction between the dsDNA and ssDNA segments of thetarget DNA where the first nucleotide would be incorporated. (b) Captureof a blocked primer/template under an applied voltage (trans sidepositive) threads the ssDNA into the pore and perches the dsDNA abovethe vestibule. This occurs because the loop at the end of the blockingprimer is too large to enter the vestibule. The current reports captureof the complex in this state. (c) Under the applied voltage, the ssDNAsegment advances in the pore toward the trans-side and processivelyunzips base-pairs between the blocking primer and the template. Theenergy cost of releasing each base pair independently is small (about2.5 kcal/mol), so it proceeds rapidly under force. During this unzippingprocess the current is the same as in (b) because the dsDNA segmentcannot enter the vestibule. (d) Release of the blocking primer followingunzipping. Absent the blocking primer, the dsDNA segment of the targetDNA can enter the pore vestibule. This results in a measurable reductionin current that signals release of the blocking primer and activation ofthe target DNA. (e) Voltage reversal exposes the activated dsDNA/ssDNAjunction for enzyme binding. By reversing voltage, the negativelycharged DNA is driven back into the cis compartment. (f) Absent theblocking primer, enzymes can bind to the DNA at the targeted position(the dsDNA/ssDNA junction in this example). (g) Probing for bound enzymeor DNA modification. Following a defined amount of time (typicallyhundred of microseconds to seconds), the voltage can be reversed onceagain to its original polarity, thus pulling the DNA back into thenanopore. Current readout can be used to determine if an enzyme has beenbound (shown) or if the DNA duplex terminus has been modified (notshown). If the result is negative, steps (e)-(g) can be repeated.

Example II Enzyme Catalysis is Prevented by a Blocking Primer

For an illustration of this method, see FIGS. 2( a) through 2(g). (a) Inthis scenario, the blocking primer is bound to the primer/template inbulk phase. Structure of the ternary complex permits binding of theenzyme to the target DNA but catalysis and processing along the templateare prevented. (b) Capture of a blocked primer/template under an appliedvoltage (trans-side positive) threads the ssDNA into the pore andperches the dsDNA above the vestibule. This occurs because the loop atthe end of the blocking primer is too large to enter the vestibule. Thecurrent reports capture of the complex in this state. (c) Under theapplied voltage, the ssDNA segment advances in the pore toward thetrans-side and processively unzips base-pairs between the blockingprimer and the template. The energy cost of releasing each base pairindependently is small (about 2.5 kcal/mol), so it proceeds rapidlyunder force. During this unzipping process the current is the same as in(b) because the dsDNA segment cannot enter the vestibule. (d) Release ofthe blocking primer following unzipping results in activation of thecomplex. Unlike the scenario disclosed in FIG. 1, the dsDNA segment ofthe target DNA cannot enter the pore vestibule when the blockdissociates because the bound enzyme is too large to enter. Thus theaverage current does not change. (e) Reducing the applied voltagepermits the enzyme to proceed. There remains sufficient ionic currentfor analysis. (f) The template strand is copied to completion. (g) Thecomplex dissociates and the nanopore is now ready to capture andactivate another DNA target (see step a).

Example III Enzyme Catalysis is Activated by Injection of Mg²⁺ Across aNanopore

For an illustration of this method, see FIGS. 3( a) through 3(c). (a) Inthis example scenario, the cis compartment contains all componentsnecessary for DNA polymerase activity except for Mg²⁺. Thus, nocatalysis can take place. (b) When voltage is applied (trans-side +),Mg²⁺ is driven across the pore into the cis compartment. (c) When aDNA-polymerase complex is captured by the pore, the Mg²⁺ concentrationin the volume immediately adjacent to the pore is sufficiently high topermit Mg²⁺ occupation of the two critical loci in the enzyme'scatalytic site. Polymerization of the copied strand can then occur.Ternary complexes in the bulk phase cannot catalyze DNA synthesisbecause the Mg²⁺ concentration distal from the pore is essentially zero.This scenario could be applied to other substances that are required forDNA synthesis and that are small enough to permeate the nanopore undercontrolled conditions.

Example IV Measuring Polymerase Activity Using a Biological Nanopore,α-Hemolysin

The polymerase activity of DNA polymerase I is largely contained in asmaller structure called the Klenow fragment. In this application, theKlenow fragment is allowed to bind to a strand of DNA (the template)that has undergone complementary base pairing with a primer of definedbase sequence. The protein is drawn to the pore and the ionic currentthrough the pore is thereby reduced. Two different enzymatic functionscan be monitored. 1) When the protein is released from its binding siteon the primer-template complex, a characteristic transient reduction ofionic current is produced. 2) When the enzyme is supplied by theappropriate dNTP substrate, a characteristic lengthening of theresidence time of the enzyme in the pore is produced. Incorrect dNTPsubstrates do not alter the residence time.

Example V Detecting Ligand Binding to a Receptor Protein

The cytoplasmic estradiol receptor is covalently linked to a 100 mer ofpolyaspartic acid by formation of an appropriate covalent bond, such asthat produced by a cross-linking agent. The receptor is positioned at a3 nm diameter silicon nitride pore by the electric field acting on thepolyaspartic acid in its anionic form. The pore has a monolayer of abifunctional alkyl sulfide attached to a gold layer on the pore. Afterpositioning, the receptor is covalently bonded to the pore by formationof disulfide bonds between the alkyl groups on the pore and cysteinegroups on the receptor. When estradiol is present, it binds to the highaffinity site on the receptor and alters ionic current though the pore,thereby providing a means of detecting this steroid hormone withsingle-molecule sensitivity.

Example VI Detecting Glucose Oxidase Activity

Following the procedure outlined in Example 2, a glucose oxidasemolecule is attached to a silicon nitride pore. When glucose is present,the enzymatic action produces detectable transient changes in the ioniccurrent through the pore as the glucose binds to the active site,oxidation, and release of products.

Example VII Monitoring Ribosome Function

A ribosome preparation is exposed to a specific mRNA in the presence ofa commonly used translation system such as cytosolic extract of E. coli.The system is maintained near 0° C. in order to inhibit ribosomefunction. Alternatively ribosomes may be inactivated by excluding arequired cofactor such as an elongation factor or tRNAs. When a singleribosome attaches to the mRNA, it can be positioned at the pore bydrawing the mRNA through the pore by the action of a transmembranevoltage of 100 mV or more. The mixture is then rapidly warmed to 25° C.to initiate protein synthesis or addition of a required cofactor. Theindividual steps of protein synthesis are then monitored by the combinedeffects on ionic current that are produced by mRNA being drawn throughthe pore by the ribosome action, and cyclic conformational changes ofthe ribosome as it proceeds through the steps of translation.

Example VIII Positioning an α-Hemolysin Channel in a Solid State Pore

Alpha hemolysin channels in the form of heptamers are assembled inliposome membranes. After assembly is complete, DNA 100 mers having astreptavidin molecule at one end are added and a transient membranepotential is produced across the liposome membrane, positive inside. Oneway to do this is to add a salt having a cation that can permeate thehemolysin channel and an anion that is impermeable due to its size. Themembrane potential draws the free end of the hairpin into the pore.Because of the streptavidin structure, the DNA cannot pass through thepore, but instead forms a complex with the hemolysin. The heptamer withits attached DNA strand is then isolated by published procedures, andadded to the cis side of a silicon nitride membrane with a 5 nm pore. Avoltage of 100 mV or more is applied, and electrophoresis draws the DNAstrand protruding from the stem of the hemolysin heptamer into the pore.The hemolysin heptamer is then covalently attached to the pore asdescribed in the Examples. The guiding DNA strand is then removed byreversing the polarity of the applied potential, and thehemolysin-silicon nitride membrane can then be used as a high resolutionnanopore for biosensor applications.

Example IX

Feedback Control of a Single Tethered DNA Molecule Suspended in aNanopore to Repeatedly Probe DNA-binding Enzymes In the biologicalnanopore setup, a planar lipid bilayer is created across a 50-100 μmteflon aperture in a KCl solution, and a single α-hemolysin proteinchannel self-inserts into the planar lipid. The channel (pore) is 15 nmin length and varies in diameter. The cis-opening of the pore is 2.6 nmwide, opening to a 3.6 nm vestibule before narrowing to a limiting 1.5nm width at the beginning of the stem. The remainder of the stem up tothe trans-opening is 2 nm wide. The vestibule is large enough fordouble-stranded DNA (dsDNA) to enter, but the limiting stem is just wideenough for single-stranded DNA (ssDNA) to pass through. AgCl electrodesare used to apply a potential across the bilayer that produces an ioniccurrent through the pore (FIG. 12). The field created by this voltagepulls the negatively charged phosphate backbone of the ssDNA or RNAthrough the pore, passing from the cis side to the trans side of thepore with the trans-side voltage positive. As molecules translocate, thepore becomes partially blocked by the translocating molecule, causing adrop in current. These translocation events can be characterized by theamplitude of the attenuated (blockade) current and the time the moleculespends in the pore, defined as the dwell time. A schematic of thenanopore system and an example DNA translocation event is shown in FIG.13. The DNA shown in FIG. 13 has single and double-stranded segments,with the double-stranded segment as a 20 base pair hairpin (20 bphp).The DNA is captured by the single-stranded end into the nanopore, andtranslocates once the voltage field force causes the hairpin to unzipwithin the vestibule. This configuration has utility towards a part ofthe instant invention. The utility of the double-stranded segment isthat it extends the dwell time (by stopping translocation) of the DNA,briefly, until the voltage shears the segment into single stranded DNAand the DNA translocates. Additionally, longer double-stranded segmentsyield longer dwell times at a given voltage. In contrast, for ssDNA orRNA, translocation rates reach up to 2 nucleotides/μsec with no pausesin translocation under capture-level voltages.

We note that the double-stranded segment may alternatively be formed byannealing a primer DNA segment, with the complementary bases, to the endof single-stranded DNA. The key is that, in our configuration, thecaptured DNA molecule must have single and double-stranded segments.This structure facilitates capture and retention: the single-strandedend is captured, and the double-stranded end increases the dwell time,providing time to detect capture and react by reducing the voltage to ahold level (explained in more detail below). Another key reason forusing this DNA structure is that the enzyme exploited in our proposedapproach binds to the DNA precisely at the single-to-double strandedjunction of the DNA.

Example X Nanopores and Enzymes

Recently, we have used biological nanopores to probe the interaction ofenzyme with a captured DNA molecule. Under an applied voltage, the ssDNAend of enzyme-bound DNA is captured in the nanopore, with the enzymeresiding on top of the nanopore being too large to translocate throughit. Kinetics of Escherichia coli exonuclease I (Exol) binding to ssDNAhas been quantified using voltage ramps for nanopore-based forcespectroscopy. Specifically, upon detection of capture of ssDNA, voltageis automated to briefly hold the ssDNA-ExoI complex, then implement avoltage ramp until Exol dissociates and the ssDNA translocates throughthe pore. The time-to-dissociation under the applied voltage ramp is inturn used to estimate binding rate constants.

Previously (see Benner, et al. (2007) Nature Nanotechnology, 2: 718-724)we have explored the interaction of DNA with the Klenow fragment (KF) ofEscherichia coli DNA polymerase I. In the absence of KF, capture andsubsequent unzipping of 14 bphp at constant 180 mV reveals blockadeswith 20 pA mean amplitude and 1 msec median dwell time (FIG. 14 a).Addition of 2 μM KF yielded a new population of events attributable tobinary complexes (DNA/KF) with higher mean amplitude (23 pA), andresulted in an event plot (FIG. 14 b II) with a longer dwell time (3msec median of all events). Addition of 200 μM deoxyguanosinetriphosphate (dGTP), the dNTP complementary to the DNA template base inthe KF catalytic site, extended the dwell time of the new population to133 msec median, attributable to a higher stability bond within ternarycomplexes (DNA/KF/dGTP).

Our tethered DNA configuration described in the next section leverages asignifycant structural feature exhibited by KF-bound DNA events (with orwithout the complementary dNTP, that is, binary or ternary complexes),now described. Closer investigation of the binary and ternary complexblockades revealed a two-step pattern in greater than 90% and 97% of theblockades, respectively. The first step has a 23 pA mean amplitude,followed by a brief (1 msec median dwell time) second step, referred toas the terminal step at 20 pA mean amplitude. It was demonstrated thatthe transition from step one to step two resulted in dissociation of KF(for binary and ternary complexes) from DNA, followed by hairpindropping into the pore vestibule until translocation occurred. Thus, theterminal step kinetics are precisely the DNA duplex unzipping kinetics.

The consistent presence of the terminal step within enzyme-bound DNAevents is mechanistically of importance to our invention. In particular,for an enzyme-bound DNA complex captured in the nanopore under aconstant voltage, the terminal step makes it possible to detect inreal-time that enzyme has dissociated from the DNA, on the basis of thechange in amplitude (from 23 pA to 20 pA at 180 mV in our recent workwith KF).

Example XI Detection and Control of DNA and KF-Bound DNA in a Nanopore

In this approach, the voltage control logic is programmed using a finitestate machine (FSM) within the LabVIEW 8 software, and the FSM logic isimplemented on a field-programmable gate array (FPGA) hardware system.Our first implementation of FSM/FPGA voltage control demonstratede_cient automated detection of individual ternary complexes, based onthe characteristic 23 pA amplitude and a dwell time of at least 20 msec.For all events that remained within the threshold range of 21.2-26.8 pAfor 20 ms, the voltage was reversed to expel the complex back into thecis chamber, rather than waiting (>100 msec median dwell time) fordissociation of enzyme and DNA translocation to the trans side. Thecontrol logic had the e_ect of concentrating the dwell time of thedetected ternary complex events, from a median dwell time of 123 msec(235 msec interquartile range (IQR)) without FSM/FPGA control, to amedian dwell time of 23 msec (0.3 msec IQR) with FSM/FPGA control. Sinceless than 2% of DNA and binary events were longer than 20 msec, thewaiting period of 20 msec ensured that nearly all controlled events wereternary complexes.

In our second implementation of FSM/FPGA voltage control, wedemonstrated efficient automated detection of individual DNA complexes(no KF enzyme present in cis-chamber), based on the characteristic 20 pAamplitude (Wilson et al. (2008) Rapid finite state machine control ofindividual DNA molecules in a nanopore. In International Conference onBiomedical Electronics and Devices (BIODEVICES), to appear, Madeira,Portugal). For all events that fell within a threshold range of 20±2.8pA, the voltage was promptly reduced to extend the DNA dwell time. In asecond experiment, for all DNA events that fell within a thresholdaround the 20 pA level, the voltage was promptly reversed to expel theDNA back into the cis chamber prior to translocation. Bothimplementations (detecting and reacting to enzyme-bound DNA events anddetecting and reacting to enzyme-free DNA events) were foundationalachievements, and prompted us to attempt to detect and discern betweenboth types of events individually, and in real time.

Example XII Equipment

A patch-clamp amplifier, Molecular Devices AxoPatch 200B, regulates theapplied voltage and measures the ionic current through the channel. Thedata are recorded using the Molecular Devices Digidata 1440A digitizer,sampled at 50 kHz and low-pass filtered at 5 kHz with a four-pole Besselfilter. One of our stations uses a different patch clamp, the A-MSystems Model 2400.

Example XIII Control Logic: Hardware and Software

The voltage control logic is programmed using a finite state machine(FSM) within the LabVIEW 8 software. The FSM logic is implemented on afield-programmable gate array (FPGA) hardware system, NationalInstruments PCI-7831R. An FPGA is a reconfigurable hardware platformthat permits fast measurement and voltage reaction times (1 μsec outputsample time). An FSM is a logic construct in which program execution isbroken up into a series of individual states. Each state has a commandassociated with it, and transitions between states are a function ofsystem measurements. Measurements of the pore current are processed andpassed to the FSM as inputs. Changes in the FSM control logic are madeas necessary, without the need to re-compile and re-route the design torun on the FPGA. This achieves a balance between speed and flexibility,by enabling the system to react to events on the order of a microsecond,while also allowing for the control logic to be reconfigured asnecessary between experiments.

Example XIV Filtering and Thresholding Ionic Current

Our control logic requires efficient detection of ionic currentblockades (events) that result from DNA alone or KF-bound DNA. Further,the logic must be able to efficiently distinguish between these twoevent types. At 180 mV, mean amplitudes for DNA alone and KF-bound DNAare 20 pA and 23 pA, respectively; a difference of 3 pA. To distinguishDNA alone from KF-bound DNA events in real time, the incoming currentsignal on the FPGA is filtered and thresholded.

Threshold levels are determined a priori, by constant voltageexperiments with the biological components to be detected in the cischamber. In our experiments with KF, amplitude thresholds consistentwith KF-bound or KF-free event amplitudes were identified at 180 mV and150 mV. At 180 mV, for example, the threshold identified and used todetect DNA alone events was 20±2.8 pA; the threshold identified and usedto detect KF-bound DNA events in was 24±2.8 pA. In our experiments todate, one or two thresholds have been implemented at a time. In futurework, more than two thresholds may be utilized at the same time, todistinguish multiple macromolecular states that are known to differbased on the attenuated amplitude.

Filtering is used to mitigate noise. Since the ionic currentpeak-to-peak noise routinely exceeds 3 pA at 180 mV, DNA alone andKF-bound DNA events would not be reliably distinguishable by monitoringthe raw current amplitude. By filtering the current amplitude, we havedemonstrated detection of DNA alone events and KF-bound DNA events inreal time. A windowed mean filter has been used in our experiments sofar, including in our invention's initial demonstration shown in Section2.3. Recently, a superior exponentially-weighted mean filter wasidentified and will be used in new experiments. Details on the twofilters are given below.

Example XV Moving Average Filter

Every 5.3 μsec, the FPGA samples the ionic current and computes awindowed mean amplitude, using a window size of 0.75 msec. If the meanenters a chosen threshold range, the FPGA detects entry and continues tomonitor the mean, re-checking the threshold every 0.2 msec. If the meanremains within the threshold range for four consecutive checks, the FSMlogic diagnoses the blockade as an event type known to be consistentwith the chosen threshold.

In the absence of a change in voltage, the expected time delay betweenthe start of an event and diagnosis of an event is 1.35 msec; 0.75 msecfor the windowed mean to first enter the threshold, and 0.6 msec forthree more confirmed tests. In practice, the diagnosis time ranges from1.1 to 2.5 msec. The mean filter was implemented in our invention'sinitial demonstration (detailed below).

Example XVI Exponentially-Weighted Moving Average Filter

Through post-experiment analysis, our mean filter was shown to falselydetect terminal steps within ternary events. Specifically, the FSM/FPGAwas programmed to detect ternary level amplitudes, wait until theterminal step, and upon detection of the terminal step, reverse thevoltage to expel the unbound DNA into the cis chamber. Examination ofthe data showed voltage reversal for many events in which no terminalstep was clearly present, although the presence of terminal steps internary events is high (97%) with no voltage reversal.

To improve the FSM's robustness to false detections of terminal steps,an exponentially-weighted moving average (EWMA) filter is now beingexplored to replace the mean filter. The EWMA filter represents adigital implementation of an analog RC filter commonly used for signalsmoothing in electrical engineering applications. The filter calculatesa moving average that places exponentially less significance on pastsamples and allows the filtered signal to better track the real signal.EWMA filtering also performs signal smoothing more efficiently than asimple moving average due to its recursive implementation:ī(t)=(1−α)i(t)+αī(t−1),  (1)

-   -   where i and ī are unfiltered and filtered current signals,        respectively, and t is the sample number. Filtering the data        from the terminal step detection experiments offline, with        α=0.9, showed a substantial improvement in robustness to false        positives over the mean filter. As with the mean filter, four        consecutive threshold tests will be used for event diagnosis,        waiting 0.2 msec between threshold tests.

In the absence of a change in voltage, the expected time delay betweenthe start of an event and diagnosis of an event is 0.7 msec; 0.1 msecfor the EWMA to first enter the threshold, and 0.6 msec for three moreconfirmed tests. More rigorous evaluation of EWMA detection times willbe part of our ongoing work.

Example XVII Time Scales for Changing the Voltage Field Force

When the magnitude of the voltage across the membrane changes, acapacitive transient is superimposed on the measured ionic current. Thetransient is present in all alpha-hemolysin nanopore studies thatinvolve voltage change (see, for example, Bates et al. (2003) supra),and necessarily masks some information in the measured current for adefined and manageable segment of each event. In our invention, thetransient implies that, when the control logic is programmed to diagnosean event type after a voltage change, the filtered current amplitudewill not enter a chosen threshold(s) for event diagnosis until thetransient has sufficiently settled.

The settling time for the transient is proportional to the net change involtage. In the voltage control experiment, the changes in appliedvoltage are from 180 mV to −50 mV, and −50 mV to 180 mV. For a netchange of 230 mV (absolute value), we observe that 98% of transientshave su_ciently decayed for accurate thresholding after 2.5 msec. In ourinitial tethered DNA experiments, voltages changes were 200 mV and 170mV (absolute value). Transients resulting from voltage changes areobservable in FIGS. 17-18.

In the presence of a change in voltage, the time required for diagnosisof an event (as a DNA event or an enzyme-bound DNA event) is expected tomatch the voltage transient settling time. This is because the transientsettling time is typically longer than the time required for thefiltered amplitude to converge onto the measured ionic current signal.Thus, diagnosis time is expected to be at most 2.5 msec for voltagechanges of 230 mV (absolute value), and less than 2.5 msec for smallervoltage changes.

Example XVIII Tethered DNA Configuration

In our initial tethered DNA experiments, a single DNA 20 bphp wascaptured in the pore, tethered, and threaded back and forth through thepore under voltage control for repeated KF binding and unbinding to thess-ds junction in the cis chamber. In the experiment, 1 μM 100 mer DNA,5 mM MgCl₂,2 μM KF, and 200 μM of dGTP were present in the cis well ofthe pore. Thus, each event results from DNA alone or a ternary complexcaptured in the nanopore.

The DNA oligomer is designed for thethering. Specifically, the 3′ end isformed into a 20 base pair hairpin, and 2 μM of 20 mer primercomplementary to the 5′ end is present in the trans chamber. Uponcapture of the 5′ end, voltage is reduced to hold the DNA in the pore,but not unzip the 3′-end hairpin in the vestibule (if an unbound DNAmolecule was captured) or dissociate KF/dGTP from the ss-ds junction (ifa ternary complex was captured). After a su_cient time period, the 20mer primer anneals to the 5′ end, creating a 20 mer duplex on the transside of the pore. Details of our initial experiments are now provided.

In the experiment, 180 mV applied voltage was used to capture each DNAmolecule in the pore with the 5′ end translocating into the transchamber. When a DNA event (threshold of [15.75, 21.25] pA) or a KF-boundDNA event (threshold of [21.25, 26.75] pA) was diagnosed using the meanfilter, the FSM reduced the potential to 50 mV, to hold the molecule inthe pore but not unzip the hairpin or dissociate KF/dGTP. The 50 mV holdvoltage was applied for 20 sec, a period sufficient for the 20 merprimer to anneal to the 5′ end of the DNA in the trans chamber. Theinitial tethering phase of a captured DNA molecule is shown in FIG. 15.

After 20 sec, the FSM reversed the voltage to −20 mV, forcing the DNAtoward the cis side of the pore with enough force to abut the 5′ duplexagainst the trans-side end of the channel, and dangle the ss-ds junctionof the 3′ end hairpin into the cis chamber. The −20 mV voltage was foundto be small enough to not unzip the 5′-end primer duplex. The amount oftime at the −20 mV voltage is referred to as the fishing time t_(fish),measured in seconds. Application of −20 mV for tfish seconds is referredto as the fishing mode of the control logic.

After t_(fish)=5 seconds at −20 mV, the FSM changed the voltage to 180mV, then monitored (thresholded) the mean filtered amplitude to diagnosethe identity of the molecule in the pore as either DNA alone orenzyme-bound DNA. If unbound DNA was diagnosed ([15.75, 21.25] pAthreshold), voltage was revered to −20 mV to restart the fishing mode.Otherwise, the FSM continued to monitor the filtered amplitude. Within aKF/dGTP-bound event, upon diagnosis of the terminal step ([15.75, 21.25]pA threshold), voltage was reversed to −20 mV to restart the fishingmode.

Application of 180 mV until unbound DNA is diagnosed (by DNA alone or byreaching the terminal step of an enzyme-bound event) is referred to asthe probing mode of the control logic. The first nine fish-then-probeactions within a tethered DNA experiment are displayed in FIG. 16. Oncethe DNA is tethered, and the FSM logic begins the fish-then-probe cycle,only the unbound DNA threshold is used for diagnosis, of unbound DNA orof a terminal step within and enzyme-bound DNA event. The FSM logicrepeats the fishing mode then probing mode cycle until the tethered DNAmolecule translocates through the pore, and the open channel current isdetected. DNA translocates if the 3′-end hairpin is unzipped or if the5′-end duplex is unzipped. We expect that DNA translocation is mostlikely to occur by unzipping the 3′-end hairpin, since unzipping at 180mV can happen faster than DNA event diagnosis. The −20 mV voltage, onthe other hand, is less likely to unzip the 5′-end duplex, even forfishing times on the order of minutes. Post experiment analysis can beused to determine the frequency of DNA translocation in probing modeversus fishing mode. When the tethered DNA translocates and currentreturns to the open channel value, the FSM resets and monitors thecurrent for another event to tether a new DNA molecule.

In a second experiment a lower capture and probing voltage of 150 mV wasused, and a faster fishing time of t_(fish)=0.521 seconds was used.Based on experiments with DNA alone and DNA with KF and dGTP at constant150 mV, the unbound DNA threshold was set to [7.5, 15.5] pA and theKF/dGTP-bound DNA threshold was set to [19,27] pA. Fishing and probingmodes are shown in FIG. 17, where probing reveals a DNA alone event.Fishing and probing modes are shown again in FIG. 18, where probingreveals an enzyme-bound DNA event. The FSM captured and tethered eightindependent DNA molecules. In total, 337 enzyme-bound DNA eventsoccurred in probing mode over a time period of 380 seconds. Analysis ofthe data shows the FSM/FPGA correctly diagnosed the terminal step inthese events 72% of the time. In the remaining 28%, fishing wasrestarted before a terminal step actually occurred in the enzyme-boundDNA event (referred to as a false positive). Offline analysis showedthat the EWMA filter resulted in zero false positives in this data.Online implementation of the EWMA filter in future tethered DNAexperiments will be used to gauge and improve the robustness of thefilter to false positives. An “unbound-DNA check” mechanism can beexplored to rule out/minimize false positives. The mechanism works asfollows: at the end of each probing mode, fish for a period too short toexpose the ss-ds junction in the cis-chamber, then re-probe to ensurethe DNA is unbound; if unbound, being fishing for period t_(fish); ifbound, wait until terminal step detected. Identification of the brieffishing period used to confirm that the DNA is unbound will be part ofour ongoing work.

Example XIX Rapid Detection and Control to Probe Individual DNA andEnzyme-Bound DNA Molecules in a Nanopore

In the biological nanopore setup, a planar lipid bilayer is createdacross a 20 μm TELON aperture in a KCl solution. A single α-hemolysinprotein channel is inserted into the planar lipid. The channel (pore) is15 nm in length and varies in diameter. The cis-opening of the pore is2.6 nm wide, opening to a 3.6 nm vestibule before narrowing to alimiting 1.5 nm width at the beginning of the stem. The remainder of thestem up to the trans-opening is 2 nm wide. The vestibule is large enoughfor double-stranded DNA (dsDNA) to enter, but the limiting stem is justwide enough for ssDNA to pass through. Across the bilayer, AgClelectrodes are used to apply a potential that produces an ionic currentthrough the pore (FIG. 12). The field created by this voltage pulls thenegatively charged phosphate backbone of the ssDNA or RNA through thepore, passing from the cis side to the trans side of the pore with thetrans-side voltage positive. As molecules translocate, the pore becomespartially blocked by the translocating molecule, causing a momentarydrop in current. These translocation events can be characterized by theamplitude of the blockade current and the time the molecule spends inthe pore, defined as the dwell time. The DNA used in the experimentspresented here are comprised of ssDNA and dsDNA segments. Specifically,for the non-FPGA experiments disclosed herein, a 14 base pair hairpin(14 bphp) 67 nucleotides in total length was used. For the rest of theexperiments, a DNA oligomer that is 79 nucleotides total in length, witha 20 bphp was used. The hairpin was formed by folding the 3′ end overitself, creating 14 or 20 base pairs. The hairpin is thus thedouble-stranded segment, with the single-stranded segment 35 nucleotideslong for both the 14 and 20 bphp (4 unpaired bases in thedoubled-stranded end loop). Upon capture of the ssDNA end, the hairpinenters the pore vestibule and remains until the hairpin is unzipped. Aschematic of the nanopore system and an example 20 bphp translocationevent is illustrated in FIG. 13.

Correlations between the ionic current amplitude and features ofindividual DNA or RNA molecules translocating through the pore has beenshown through various assays using _-hemolysin nanopores. A near directcorrelation between the number of molecules passing through the pore andthe number of current drops has been demonstrated. Homopolymers of ssDNAand block copolymers of RNA are also distinguishable based on themeasurable differences in the blockade current amplitude or kinetics.However, translocation rates are too fast (up to 2 nucleotides/μsec) forsequencing individual nucleotides in heterogeneous single-strandedpolymers using existing biological nanopores. Here and in other studies,DNA with single and double stranded segments is used to increase thedwell time of nucleotides in the pore (0.5-5 msec, depending on appliedvoltage and dsDNA segment length). For example, blunt-ended hairpins,those with no single-stranded overhang, ranging from 3 to 9 bases longare used in Vercoutere et al (2001; Nat. Biotechnol, 19(3):248-252, andVercoutere et al. (2003) Nucleic acids research, 31:1311-1318), wheremachine learning methods were applied to the extended dwell time eventsto identify (sequence) the terminal base pair made up of the 3′ and 5′ends of the ssDNA.

Example XX Voltage Control Using FSM/FPGA

The nanopore system is setup in a 0.3 mM KCl solution. A patch-clampamplifier, Molecular Devices AxoPatch 200B, regulates the appliedvoltage and measures the ionic current through the channel. The data arerecorded using the Molecular Devices Digidata 1440A digitizer, sampledat 50 kHz and low-pass filtered at 5 kHz with a four-pole Bessel filter.

The voltage control logic is programmed using a FSM within the LabVIEW 8software. The FSM logic is implemented on a field-programmable gatearray (FPGA) hardware system, National Instruments PCI-7831R. An FPGA isa reconfigurable hardware platform that permits fast measurement andvoltage reaction times (1 μsec output sample time). An FSM is a logicconstruct where program execution is broken up into a series ofindividual states. Each state has a command associated with it, andtransitions between states are a function of system measurements.Measurements of the pore current are processed and passed to the FSM asinputs. Changes in the FSM control logic are made as necessary, withoutthe need to re-compile and re-route the design to run on the FPGA. Thisachieves a balance between speed and flexibility, by enabling the systemto react to events on the order of a microsecond, while also allowingfor the control logic to be reconfigured as necessary betweenexperiments.

Example XXI FSM Monitoring of Mean Filtered Current for DNA andEnzyme-Bound DNA Event Diagnosis

Blockade events, quantified by the blockage current and dwell time, canbe detected and monitored in real time using the FSM/FPGA. A mean filterapplied to the incoming current signal on the FPGA removes a largeportion of the peak-to-peak noise. Specifically, every 5.3 μsec, theFPGA samples the ionic current and computes a windowed mean amplitude.The FPGA tests if the mean is within a pre-specified range and thencontinues to test the mean every 0.2 msec after initial detection. Ifthe mean enters and remains within this range for four consecutivetests, the FSM logic diagnoses the blockade as a DNA hairpin event. Thetime delay between a DNA translocation event and diagnosis of a DNAtranslocation event is nominally 1.35 msec; 0.75 msec for the windowedmean to first enter the 17.2 to 22.8 pA range, and 0.6 msec for threemore confirmed tests, and 0.65 ms of computational delay. The meanfiltered current is used for DNA event diagnosis and triggers thetransitions between states in the FSM control logic.

The FSM control logic has been used to discern between DNA alone orDNA/enzyme complex using the nanopore system. Additionally, enzymedissociation from DNA can be detected and reacted to in real time usingthe FSM to detect the terminal steps present in the current signal. Theability to detect both DNA and DNA/enzyme complex in the pore can permitthe real-time identification of the base at the junction betweensingle-stranded and double-straned DNA when KF is bound to a DNA hairpinand the correct nucleotide is present in the system, as detailed in thisreport.

Furthermore, the detection and control of single DNA hairpin moleculescan be expanded to include repeated capture of KF using a single copy ofDNA. One base can be identified when KF is pulled off a DNA hairpinusing a nanopore. Repeated capture and dissociation of KF from the samecopy of DNA can allow many bases to be sequenced provided a method forsingle-base ratcheting polymerase reaction is found. Current sequencingmethods are limited to read lengths of around one kilobase (1000 basepairs identified), but a nanopore-based sequencing method has potentialfor much longer read lengths when compared to traditional bulksequencing methods.

The bulk of the future work is dedicated to improving the detectionrobustness by increasing the signal-to-noise of the current signalthrough improved filtering and use of longer DNA hairpins. Also, adouble-checking scheme to ensure the enzyme has dissociated will beimplemented. Experiments that vary the concentration of KF and dNTP willalso be performed to find the detection limit of different complexes.

Example XXII Detection of Molecular Complexes

The interaction of DNA with Klenow fragment (KF) of Escherichia coli DNApolymerase I can be probed with the nanopore system. In the absence ofKF, capture and subsequent unzipping of 20 bphp at constant 180 mVreveals current blockades with 20 pA mean amplitude and 4 msec mediandwell time. Addition of KF and the dNTP complementary to the DNAtemplate base in the KF catalytic site yielded a substantial increase inblockade dwell times (110 msec median lifetime for dGTP), attributableto ternary (DNA/KF/dGTP) complexes. Closer investigation of suchblockades revealed a two-step pattern in greater than 97% of theblockades, the first step at 24 pA mean amplitude, and the second(terminal) step at 20 pA mean amplitude, lasting 4 ms consistent withthe hairpin kinetics alone. It was demonstrated that the transition fromstep one to two resulted in dissociation of KF from DNA first, followedby the hairpin dropping into the pore vestibule until unzippingoccurred. As a initial effort at voltage control of enzyme-bound DNA,e_cient automated detection (<3 msec) of individual ternary complexeswas demonstrated, based on the characteristic 24 pA amplitude andtruncation of the blockade time by voltage reversal after 20 msec. The20 msec cutoff was used because 60% of events are longer than 20 msec inthe presence of the correct dNTP, while only 2% of events are longerthan 20 msec and in the detection range absent the correct dNTP, showingthat events longer than 20 msec usually correspond to ternary complexevents (FIG. 14). Detection was based on the mechanism described inSection 1.2.2 for calculating the windowed mean using the previous 1.5msec of signal and a detection range of 17.2 to 22.8 pA. The basis forchoosing this range is that ˜20 pA is the median amplitude for 14 and 20bphp events at 180 mV as well as the terminal step (FIG. 19).

The ability to diagnose individual events in real time shows potentialfor extending this system to sequencing. A single long dwell time event(>20 msec) gives high probability of a ternary complex event. Based onthe dNTP present in the system, the identity of the next base to beadded can be identified, achieving single base sequencing. For multiplebase reads, regulation of base polymerization is necessary to step alongthe addition of nucleotides. For every base added, enzyme-bound DNApresent in the pore can be probed for the presence of ternary complex,confirming the correct dNTP is present for polymerization. In theexperiments presented here, the dNTPs are di-deoxy terminated sopolymerization is stalled, preventing more than a single base additionto the hairpin. This use of di-deoxy terminators is the foundation ofmost sequencing methods employed today.

Example XXIII Control of Individual DNA Molecules

Rapid detection (<2 msec) is based on computing a filtered meanamplitude, based on the last 0.75 msec of the ionic current, in realtime and monitoring the mean relative to an amplitude range consistentwith DNA hairpin blockades (20±2.8 pA). Upon detection, two methods ofvoltage control were demonstrated.

In the first method, dwell time extension is achieved by prompt voltagereduction, with the reduced voltage applied until the hairpin unzips. Ahigher voltage for capture increases the number of molecules examined,and the reduced voltage post-capture increases the dwell time to, inprinciple, facilitate sequencing. In particular, extending the life ofDNA hairpins in the pore increases the time within which a terminal baseidentification could be achieved using machine learning methods.

The second method reduces the voltage for a preset time (10 msec) andthen reverses the voltage to expel the molecule prior to hairpinunzipping. This demonstrates control authority to aggregate the dwelltimes of hundreds of blockade events. Additionally, it complementsprevious work, confirming the ability to detect both DNA-enzymeblockades and DNA hairpin blockades. Confirmation of the ability todiscern between each blockade type in real time is crucial to futurework. Ultimately, nanopore-based characterization of enzyme dynamicswill require direct detection and control of multiple DNA conformationsrelative to the enzyme, and direct control of enzyme-free DNA is aprerequisite toward developing this capability.

Direct control of ssDNA in a nanopore has been demonstrated, in whichdetection of DNA is based on monitoring the raw amplitude relative to athreshold level. Voltage level changes, comparable to those employedhere, were commanded to explore the zero and low voltage effects onssDNA-pore interactions. In contrast to thresholding the raw ioniccurrent amplitude, the windowed amplitude mean calculation used herefilters the current noise. Additionally, detection depends on the meanremaining within a preset amplitude range (<6 pA in spread) for multipleconsecutive comparisons, resulting in fewer false detections than asingle threshold comparison.

Example XXIV Experiments and Results

A demonstration of direct FSM/FPGA control of single DNA molecules in ananopore is now described. In a first experiment, the objective was toefficiently detect DNA hairpin events, one molecule at a time andincrease the blockade dwell time by lowering the applied voltage from180 mV to 150 mV upon detection. This is referred to as “dwell timeextension control”. After completing this objective, the aggregation ofthe extended blockade dwell times was sought by expelling the DNA usingvoltage reversal of −50 mV after 10 msec at 150 mV. This is referred toas “dwell time aggregation control”. The motivation was to increase thenominal hairpin dwell time, but expel the molecule before unzipping thehairpin. A tighter distribution for the aggregated dwell time events, incontrast to the distribution of the extended dwell time events, willindicate that the objective has been met.

A typical 20 bphp event at constant 180 mV voltage is shown in FIGS. 13and 21 aI. The probability histogram of the base 10 logarithm of dwelltime (FIG. 21 a III, solid bars) is unimodal, with median dwell time of2.8 msec. The median amplitude of the event plot in FIG. 21 aII is 20.9pA with an interquartile range (IQR) of 1.7 pA. Only 6% of events are inthe subset range of 13 to 18 pA (FIG. 21 aIII, open bars). For the sameexperiment at constant 150 mV voltage (data not shown), the eventscluster around a median amplitude of 14.7 pA and 87% of 150 mV eventsare in the 13 to 18 pA range. Thus, under extension and aggregationcontrol for which the voltage is reduced to 150 mV for all detectedevents, a larger percentage of blockades should have a mean amplitudewithin the 13 to 18 pA range.

Example XXV Dwell Time Extension Control (FIG. 21 b)

Upon diagnosis of a DNA hairpin event using the mean filtered current,the command voltage is reduced to 150 mV until the hairpin unzips andthe DNA translocates through the pore. Using 180 mV for capture resultsin more events than 150 mV, while reducing to 150 mV extends the life ofthe hairpin. Again, dwell time extension is useful for sequencing bymachine learning methods. The extended time can also be used to increasethe likelihood of correctly detecting DNA or DNA-enzyme configurations(states), by increasing the time during which the mean must residewithin the amplitude threshold corresponding to each state. After eachtranslocation, the FPGA resets the voltage to 180 mV. A representativeevent is shown in FIG. 21 bI. The event plot (FIG. 21 bII) pattern showsthat events faster than the nominal diagnosis time of ˜1.4 msec areuna□ected by extension control, and events with longer dwell timesconverge to the ˜15 pA mean amplitude as expected. The concave trend isalso consistent with the mean amplitude computation for each event. Inparticular, for an event at 21 pA for 1.4 msec and at 15 pA for x msec,an approximate event mean amplitude Ī is

$\overset{\_}{I} = \frac{{1.4*21} + {15*x}}{1.4 + x}$When x≈24 msec, as in FIG. 21 bI, Ī=15 pA. The fraction of events withinthe subset range 13 to 18 pA increased to 41% and is shown in the openbar histogram overlaid on the probability (filled bars) histogram (FIG.21 bIII).

Example XXVI Dwell Time Aggregation Control (FIG. 21 c)

The objective was to aggregate the dwell times of the extended events byapplying 150 mV for 10 msec upon diagnosis of a hairpin event, followedby voltage reversal of −50 mV for 5 msec. The reversal time of 5 msec isknown to sufficiently clear the DNA from the channel, prepping the porefor the next event. The aggregation control would imply a measure ofcontrol over the distribution of the events, in addition to control ofthe individual molecular events. A representative event is shown in FIG.21 cI. As before, the event plot (FIG. 21 cII) pattern shows that eventsfaster than the nominal diagnosis time of ˜1.4 msec are unaffected byaggregation control. Using the previous equation, for an event at 21 pAfor 1.4 msec and at 15 pA for 10 msec, the approximate event meanamplitude is =16 pA. Within the subset range of 13 to 18 pA, the medianis 16 pA with 0.7 pA IQR, precisely the approximate mean calculation.The fraction of events within the subset range 13 to 18 pA increased to55%, shown in the open bar histogram overlaid on the filled barprobability histogram (FIG. 21 cIII). For the subset of events, a mediandwell time of 12.4 msec is commensurate with a brief delay, required todiagnose hairpin state, plus 10 msec extension time. An IQR of 0.1 forthe open bar subset histogram indicates that the aggregation objectivehas been achieved. Regarding the impact of control on the distributionof events, 43% of all events in FIG. 21 c μl fall within the dwell timerange of 12-13 msec and the amplitude range of 13-18 pA.

Example XXVII Tethered DNA

Preliminary experiments were run with KF bound to a 20 base pair DNAhairpin (20 bphp). A single 20 bphp is threaded back and forth throughthe pore such that KF binds with the DNA multiple times. In thisexperiment, 1 μM 100 mer ssDNA, 5 mM MgCl₂, 2 μM KF, and 200 μM of dGTPwere present in the cis well of the pore. The ssDNA oligomer wasdesigned such that a 20 mer hairpin forms on the 3′ end. On the transside, there was 2 μM of a 20 base pair (20 mer) primer complementary tothe sequence at the 5′ end of the DNA hairpin in the cis side.

With voltage applied, DNA was drawn through the pore with the 5′ endtranslocating first. When a 20 pA event characteristic of a ssDNAtranslocation event was detected, the FSM reduced the potential to 50mV, a level sufficient enough to hold the molecule in the pore but notstrong enough to shear the hairpin. If a 24 pA event characteristic ofenzyme-bound DNA was detected, application of voltage was continueduntil the enzyme dissociated, leaving the bare DNA in the pore, at whichpoint the voltage was reduced to 50 mV to hold the molecule in the pore.The molecule was held in the pore for 20 sec, a time found to besufficient for the 20 mer primer to anneal to the 5′ end of the DNA at 2μM primer concentration. With both ends of the DNA consisting of 20 merdouble-stranded segments, the molecule was restrained from immediatelytranslocating. After the primer annealing waiting time, the FSM reversedthe voltage to −20 mV, pulling the DNA toward the cis side of the porewith enough force to dangle it in solution but not to shear thetrans-side primer. The voltage stayed at −20 mV for 5 sec, after whichthe FSM changed the voltage to 180 mV to diagnose the identity of themolecule in the pore; either DNA alone, DNA/KF binary complex, orDNA/KF/dGTP ternary complex. If enzyme-bound, as presumed if ˜24 pA isobserved, the FSM monitored the current signal for the 20 pA terminalstep, the point when KF has dissociated but before the DNA translocates,to reverse the voltage back to −20 mV to attempt to capture another KF.If the FSM failed to detect the DNA molecule before it translocated, thecurrent returned to the open channel current of ˜60 pA, and the FSMwould monitor the current for another DNA translocation event and repeatthe fishing process (FIG. 22). If no enzyme is captured during aparticular fishing attempt, the FSM tried fishing again until enzymecapture did occur. For the data analyzed from this experiment, five DNAcopies were captured and used to fish for KF. Long dwell time events(that is, events >20 msec) were recorded for 95.1% of fishing attemptsthough no analysis has been done to determine the number of KFdissociation events that were correctly reacted to by the FSM.

After performing the initial proof-of-concept experiments, a second runof fishing experiments were run that yielded better results. Using afishing time of 0.521 seconds, the FSM captured eight copies of the sameDNA hairpin and reacted to 337 potential KF dissociation events over atime period of 380 seconds. Post analysis of the data shows the FPGAcorrectly detected and reacted to an enzyme dissociation event for71.86% of KF captures, for example, 74 of the 337 potential dissociationevents were false positives.

Example XXVIII Mitigating False-Enzyme Dissociation Detection

In the data presented above, the dissociation of the enzyme is detectedby mean filtering the nanopore current signal and checking to see if itis within a chosen amplitude range. This method of smoothing yielded alarge number of false detections. As an improvement to this filteringscheme, an exponentially weighted moving average (EWMA) filter canreplace the mean filter that the FPGA used. The EWMA filter is a digitalimplementation of an analog RC filter, commonly used for signalsmoothing in electrical engineering applications. The filter calculatesa moving average that places exponentially less significance on pastsamples. EWMA filtering also performs signal smoothing more efficientlythan a simple moving average due to its recursive implementation.However, experimental testing still needs to be done to tune the filterfor nanopore current signal analysis.

To more robustly detect enzyme dissociation events, a KF dissociationcheck needs to be implemented to ensure fishing is being done with bareDNA. When the FPGA detects KF dissociation, it will fish for a period oftime sufficiently fast so KF will not bind and then it will check theDNA for the presence of enzyme. If only bare DNA is diagnosed (currentis ˜20 pA), then the enzyme has dissociated and the system can attemptto capture another enzyme. This check is important for performingexperiments to collect information on repeat events. For the data to bevalid and statistically accurate, each detected event must be a newenzyme binding event.

The majority of long dwell time events correspond to strong KF bindingevents, for example, the next dNTP to be added to the template strand ispresent in the nanopore system, when saturating levels of KF and thecorrect dNTP are present. Multiple long dwell time events in a rowimprove confidence in base identification because repeated sequentiallong dwell time events occur even less often when the correct dNTP to beadded is absent than when it is present. Here is where KF fishing willshow its utility. Separate work is being done to model the dwell timeevents as a Poisson process so a Phred quality score can be applied to abase identity diagnosis based on the number of repeated sequential longdwell time events. The Phred system is an accuracy metric used commonlyin DNA sequencing. For example, a 90% accurate call would be a Q₁₀ onthe Phred scale and a 99% accurate call would be Q₂₀. Q₂₀ is consideredthe standard level of quality in DNA sequencing at the time of writing.

Another method to improve the detectability of the current step at theend of enzyme events is to use a longer hairpin and run the experimentsat a higher voltage. The signal-tonoise of the channel current willimprove due to higher ion flow through the channel, making the terminalsteps more prominent.

Example XXIX Voltage Titration Experiments

A more quantitative connection between the amplitude and duration of theterminal step and the applied voltage may be made. The goals here are toreveal the repeatability of the terminal step and show how its structureis consistent with DNA alone at different voltages. An in-depthcharacterization of the terminal step allows for better control of theterminal step. Constant voltage experiments are run at four differentvoltages with DNA alone as well as DNA/KF/dNTP ternary complex, usingsaturating levels of each substrate (1 μM, 2 μM, and 200 μMrespectively). Voltages are 220, 200, 180, and 160 mV. A 24 bphp is usedrather than the 20 bphp used in the other tethered experiments to extendthe dwell time at higher voltages. Higher voltages are run first todetermine a practical upper limit for an applied voltage that yieldsdetectable terminal step event durations (1 msec).

Example XXX Terminal Step Control Experiments

As described above, it is necessary to show accurate detection andreaction to the terminal step. As stated earlier, 97% of enzyme-boundevents showed the terminal step, therefore, this is the theoreticalmaximum detection rate. Detection and reaction to the terminal step willbe shown by voltage reversal upon detection, aggregating the terminalstep duration. A high probing voltage, as used above, gives moreresolution between the bound and unbound current levels. Experiments arerun with DNA alone as well as DNA/KF/dNTP ternary complex, usingsaturating levels of each substrate. Robustness to false positives maybe shown by verifying accurate detection offline.

Example XXXI Terminal Step Control Experiments: Tethered DNAConfiguration with Fishing Time Titration

A repeat of what was achieved above is performed but with tethered DNA.Titration of the fishing time is performed to reproduce the ratio of DNAalone events to ternary complex events comparable to those in thenon-tethered DNA experiments. This information helps set limits on thefishing time to maintain representative sampling of the contents of thecis well. Experiments are run with DNA alone as well as DNA/KF/dNTPternary complex; using saturating levels of each substrate.

Example XXXII Fishing Titration Experiments

Titration of KF and dGTP are performed. The percentage of long eventsare recorded as a function of KF and dGTP concentration. Experiments arerun at the same high capture voltage as above. The same concentrationintervals for KF and dGTP as in the supplement of Benner et al (2007)

Sequence specific detection of DNA polymerase binding using ananopore-based state machine. Submitted to Nature Methods) are used:(KF=[0, 0.25, 0.5, 1.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0] μM;dGTP=[0, 0, 0, 0, 2.5, 7.5, 15, 30, 60, 120, 200] μM).

Example XXXIII Other Enzyme Studies

The FPGA/FSM nanopore system can also be used for other enzyme studies.Applying voltage ramps upon capture of DNA/enzyme complexes can producedata to calculate bond energy landscapes using voltage forcespectroscopy. Also, DNA's interaction with the pore can be characterizedusing feedback control of the applied voltage. Regulation of enzymecatalysis can be by achieved applying tension to DNA occupying the pore,counteracting the enzymes processive force.

Example XXXIV Isolation of Genomic DNA

Blood samples (2-3 ml) are collected from patients via the pulmonarycatheter and stored in EDTA-containing tubes at −80° C. until use.Genomic DNA is extracted from the blood samples using a DNA isolationkit according to the manufacturer's instruction (PUREGENE, GentraSystems, Minneapolis Minn.). DNA purity is measured as the ratio of theabsorbance at 260 and 280 nm (1 cm lightpath; A₂₆₀/A₂₈₀) measured with aBeckman spectrophotometer.

Example XXXV Identification of SNPs

A region of a gene from a patient's DNA sample is amplified by PCR usingthe primers specifically designed for the region. The PCR products aresequenced using methods as disclosed above. SNPs identified in thesequence traces are verified using Phred/Phrap/Consed software andcompared with known SNPs deposited in the NCBI SNP databank.

Example XXXVI cDNA Library Construction

A cDNA library is constructed using RNA isolated from mammalian tissue.The frozen tissue is homogenized and lysed using a POLYTRON homogenizer(Brinkmann Instruments, Westbury N.J.) in guanidinium isothiocyanatesolution. The lysates are centrifuged over a 5.7 M CsCl cushion using aSW28 rotor in an L8-70M Ultracentrifuge (Beckman Coulter, FullertonCalif.) for 18 hours at 25,000 rpm at ambient temperature. The RNA isextracted with acid phenol, pH 4.7, precipitated using 0.3 M sodiumacetate and 2.5 volumes of ethanol, resuspended in RNAse-free water, andtreated with DNAse at 37° C. RNA extraction and precipitation arerepeated as before. The mRNA is isolated with the OLIGOTEX kit (Qiagen,Chatsworth Calif.) and used to construct the cDNA library.

The mRNA is handled according to the recommended protocols in theSUPERSCRIPT plasmid system (Invitrogen). The cDNAs are fractionated on aSEPHAROSE CL4B column (APB), and those cDNAs exceeding 400 bp areligated into an expression plasmid. The plasmid is subsequentlytransformed into DH5aa competent cells (Invitrogen).

Example XXXVII Preparation and Sequencing of cDNAs

The cDNAs are prepared using a MICROLAB 2200 (Hamilton, Reno Nev.) incombination with DNA ENGINE thermal cyclers (MJ Research) and sequencedby the method of Sanger and Coulson (1975; J. Mol. Biol. 94: 441-448)using PRISM 377 or 373 DNA sequencing systems (ABI). Reading frame isdetermined using standard techniques.

The nucleotide sequences and/or amino acid sequences of the SequenceListing are used to query sequences in the GenBank, SwissProt, BLOCKS,and Pima II databases. BLAST produced alignments of both nucleotide andamino acid sequences to determine sequence similarity. Because of thelocal nature of the alignments, BLAST is used in determining exactmatches or in identifying homologs that may be of prokaryotic(bacterial) or eukaryotic (animal, fungal, or plant) origin. Otheralgorithms such as those of Smith et al. (1992; Protein Engineering5:35-51) could have been used when dealing with primary sequencepatterns and secondary structure gap penalties. The sequences disclosedin this application have lengths of at least 49 nucleotides and have nomore than 12% uncalled bases (where N is recorded rather than A, C, G,or T).

The BLAST approach searched for matches between a query sequence and adatabase sequence. BLAST evaluated the statistical significance of anymatches found, and reported only those matches that satisfy theuser-selected threshold of significance. In this application, thresholdis set at 10⁻²⁵ for nucleotides and 10⁻¹⁰ for peptides.

Example XXXVIII Extension of cDNAs

The cDNAs are extended using the cDNA clone and oligonucleotide primers.One primer is synthesized to initiate 5′ extension of the knownfragment, and the other, to initiate 3′ extension of the known fragment.The initial primers are designed using primer analysis software to beabout 22 to 30 nucleotides in length, to have a GC content of about 50%or more, and to anneal to the target sequence at temperatures of about68° C. to about 72° C. Any stretch of nucleotides that would result inhairpin structures and primer-primer dimerizations is avoided.

Selected cDNA libraries are used as templates to extend the sequence. Ifextension is performed than one time, additional or nested sets ofprimers are designed. Preferred libraries have been size-selected toinclude larger cDNAs and random primed to contain more sequences with 5′or upstream regions of genes. Genomic libraries can be used to obtainregulatory elements extending into the 5′ promoter binding region.

High fidelity amplification is obtained by PCR using methods such asthat taught in U.S. Pat. No. 5,932,451. PCR is performed in 96-wellplates using the DNA ENGINE thermal cycler (MJ Research). The reactionmix contained DNA template, 200 nmol of each primer, reaction buffercontaining Mg²⁺, (NH₄)₂SO₄, and b-mercaptoethanol, Taq DNA polymerase(APB), ELONGASE enzyme (Invitrogen), and Pfu DNA polymerase(Stratagene), with the following parameters. The parameters for thecycles are 1: 94° C., three minutes; 2: 94° C., 15 seconds; 3: 60° C.,one minute; 4: 68° C., two minutes; 5: 2, 3, and 4 repeated 20 times; 6:68° C., five minutes; and 7: storage at 4° C. In the alternative, theparameters for primer pair T7 and SK+ (Stratagene) are as follows: 1:94° C., three minutes; 2: 94° C., 15 seconds; 3: 57C, one minute; 4: 68°C., two minutes; 5: 2, 3, and 4 repeated 20 times; 6: 68° C., fiveminutes; and 7: storage at 4° C.

The concentration of DNA in each well is determined by dispensing 100 mlPICOGREEN quantitation reagent (0.25% reagent in 1×TE, v/v; MolecularProbes) and 0.5 ml of undiluted PCR product into each well of an opaquefluorimeter plate (Corning Life Sciences, Acton Mass.) and allowing theDNA to bind to the reagent. The plate is scanned in a Fluoroskan II(Labsystems Oy, Helsinki, Finland) to measure the fluorescence of thesample and to quantify the concentration of DNA. A 5 ml to 10 ml aliquotof the reaction mixture is analyzed by electrophoresis on a 1% agaroseminigel to determine which reactions are successful in extending thesequence.

The extended clones are desalted, concentrated, transferred to 384-wellplates, digested with CviJI cholera virus endonuclease (MolecularBiology Research, Madison Wis.), and sonicated or sheared prior toreligation into pUC18 vector (APB). For shotgun sequences, the digestednucleotide sequences are separated on low concentration (0.6 to 0.8%)agarose gels, fragments are excised, and the agar is digested withAGARACE enzyme (Promega). Extended clones are religated using T4 DNAligase (New England Biolabs) into pUC18 vector (APB), treated with PfuDNA polymerase (Stratagene) to fill-in restriction site overhangs, andtransfected into E. coli competent cells. Transformed cells are selectedon antibiotic-containing media, and individual colonies are picked andcultured overnight at 37° C. in 384-well plates in LB/2× carbenicillinliquid media.

The cells are lysed, and DNA is amplified using primers, Taq DNApolymerase (APB) and Pfu DNA polymerase (Stratagene) with the followingparameters: 1: 94° C., three minutes; 2: 94° C., 15 seconds; 3: 60° C.,one minute; 4: 72° C., two minutes; 5: 2, 3, and 4 repeated 29 times; 6:72° C., five minutes; and 7: storage at 4° C. DNA is quantified usingPICOGREEN quantitation reagent (Molecular Probes) as described above.Samples with low DNA recoveries are reamplified using the conditionsdescribed above. Samples are diluted with 20% dimethylsulfoxide (DMSO;1:2, v/v), and sequenced using DYENAMIC energy transfer sequencingprimers and the DYENAMIC DIRECT cycle sequencing kit (APB) or the PRISMBIGDYE terminator cycle sequencing kit (ABI).

Example XXXIX Extension of Polynucleotides

At least one of the polynucleotides used to assemble a polynucleotide isproduced by extension of a cDNA clone using oligonucleotide primers. Oneprimer is synthesized to initiate 5′ extension of the known fragment,and the other, to initiate 3′ extension. The initial primers aredesigned using OLIGO 4.06 primer analysis software (NationalBiosciences) to be about 22 to 30 nucleotides in length, to have a GCcontent of about 50%, and to anneal to the target sequence attemperatures of about 55° C. to about 68° C. Any fragment that wouldresult in hairpin structures and primer-primer dimerizations is avoided.Selected human cDNA libraries are used to extend the molecule. If morethan one extension is needed, additional or nested sets of primers aredesigned.

High fidelity amplification is obtained by performing PCR in 96-wellplates using the DNA ENGINE thermal cycler (MJ Research). The reactionmix contains DNA template, 200 nmol of each primer, reaction buffercontaining Mg²⁺, (NH₄)₂ SO₄, and b-mercaptoethanol, Taq DNA polymerase(Amersham Pharmacia Biotech), ELONGASE enzyme (Life Technologies), andPfu DNA polymerase (Stratagene), with the following parameters forprimer pair selected from the plasmid: Step 1: 94° C., 3 minutes; Step2: 94° C., 15 seconds; Step 3: 60° C., 1 minute; Step 4: 68° C., 2minutes; Step 5: Steps 2, 3 and 4 repeated 20 times; Step 6: 68° C., 5minutes; Step 7: storage at 4° C. In the alternative, when using asequence inserted into a plasmid vector, parameters for the primer pair,T7 and SK+ (Stratagene), are as follows: Step 1: 94° C., 3 minutes; Step2: 94° C., 15 seconds; Step 3: 57° C., 1 minutes; Step 4: 68° C., 2minutes; Step 5: Steps 2, 3, and 4 repeated 20 times; Step 6: 68° C., 5minutes; Step 7 storage at 4° C.

The concentration of DNA in each well is determined by dispensing 100 mlPICOGREEN quantitation reagent (0.25% (v/v); Molecular Probes) dissolvedin 1×TE and 0.5 ml of undiluted PCR product into each well of an opaquefluorimeter plate (Corning Costar, Acton Mass.) and allowing the DNA tobind to the reagent. The plate is scanned in a Fluoroskan II (LabsystemsOy, Helsinki, Finland) to measure the fluorescence of the sample and toquantify the concentration of DNA. A 5 ml to 10 ml aliquot of thereaction mixture is analyzed by electrophoresis on a 1% agarose mini-gelto determine which reactions are successful in producing longersequence.

The extended sequences are desalted, concentrated, transferred to384-well plates, digested with CviJI cholera virus endonuclease(Molecular Biology Research, Madison Wis.), and sonicated or shearedprior to religation into pUC 18 vector (Amersham Pharmacia Biotech). Forshotgun sequencing, the digested fragments are separated on about0.6-0.8% agarose gels, fragments are excised as visualized under UVlight, and agar removed/digested with AGARACE (Promega). Extendedfragments are religated using T4 DNA ligase (New England Biolabs) intopUC 18 vector (Amersham Pharmacia Biotech), treated with Pfu DNApolymerase (Stratagene) to fill-in restriction site overhangs, andtransformed into competent E. coli cells. Transformed cells are selectedon antibiotic-containing media, and individual colonies are picked andcultured overnight at 37° C. in 384-well plates in LB/2× carbenicillinliquid media.

The cells are lysed, and DNA is amplified using Taq DNA polymerase(Amersham Pharmacia Biotech) and Pfu DNA polymerase (Stratagene) withthe following parameters: Step 1: 94° C., 3 minutes; Step 2: 94° C., 15seconds; Step 3: 60° C., 1 minutes; Step 4: 72° C., 2 minutes; Step 5:steps 2, 3, and 4 repeated 29 times; Step 6: 72° C., 5 minutes; Step 7:storage at 4° C. DNA is quantified by PICOGREEN reagent (MolecularProbes) as described above. Samples with low DNA recoveries arereamplified using the conditions described above. Samples are dilutedwith 20% dimethysulphoxide (1:2, v/v), and sequenced using DYENAMICenergy transfer sequencing primers and the DYENAMIC DIRECT kit (AmershamPharmacia Biotech) or the ABI PRISM BIGDYE terminator cycle sequencingready reaction kit (PE Biosystems).

In like manner, the polynucleotides of SEQ ID NOs: 1-163 are used toobtain regulatory sequences using the procedure above, oligonucleotidesdesigned for outward extension, and a genomic DNA library.

Example XL Labeling of Probes and Hybridization Analyses

Nucleic acids are isolated from a biological source and applied to asubstrate for standard hybridization protocols by one of the followingmethods. A mixture of target nucleic acids, a restriction digest ofgenomic DNA, is fractionated by electrophoresis through an 0.7% agarosegel in 1×TAE [Tris-acetate-ethylenediamine tetraacetic acid (EDTA)]running buffer and transferred to a nylon membrane by capillary transferusing 20× saline sodium citrate (SSC). Alternatively, the target nucleicacids are individually ligated to a vector and inserted into bacterialhost cells to form a library. Target nucleic acids are arranged on asubstrate by one of the following methods. In the first method,bacterial cells containing individual clones are robotically picked andarranged on a nylon membrane. The membrane is placed on bacterial growthmedium, LB agar containing carbenicillin, and incubated at 37° C. for 16hours. Bacterial colonies are denatured, neutralized, and digested withproteinase K. Nylon membranes are exposed to UV irradiation in aSTRATALINKER UV-crosslinker (Stratagene) to cross-link DNA to themembrane.

In the second method, target nucleic acids are amplified from bacterialvectors by thirty cycles of PCR using primers complementary to vectorsequences flanking the insert. Amplified target nucleic acids arepurified using SEPHACRYL-400 beads (Amersham Pharmacia Biotech).Purified target nucleic acids are robotically arrayed onto a glassmicroscope slide (Corning Science Products, Corning N.Y.). The slide ispreviously coated with 0.05% aminopropyl silane (Sigma-Aldrich, St.Louis Mo.) and cured at 110° C. The arrayed glass slide (microarray) isexposed to UV irradiation in a STRATALINKER UV-crosslinker (Stratagene).

cDNA probes are made from mRNA templates. Five micrograms of mRNA ismixed with 1 mg random primer (Life Technologies), incubated at 70° C.for 10 minutes, and lyophilized. The lyophilized sample is resuspendedin 50 ml of 1× first strand buffer (cDNA Synthesis systems; LifeTechnologies) containing a dNTP mix, [a-³² P]dCTP, dithiothreitol, andMMLV reverse transcriptase (Stratagene), and incubated at 42° C. for 1-2hours. After incubation, the probe is diluted with 42 ml dH₂O, heated to95° C. for 3 minutes, and cooled on ice. mRNA in the probe is removed byalkaline degradation. The probe is neutralized, and degraded mRNA andunincorporated nucleotides are removed using a PROBEQUANT G-50MicroColumn (Amersham Pharmacia Biotech). Probes can be labeled withfluorescent markers, Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech),in place of the radionucleotide, [³²P]dCTP.

Hybridization is carried out at 65° C. in a hybridization buffercontaining 0.5 M sodium phosphate (pH 7.2), 7% SDS, and 1 mM EDTA. Afterthe substrate is incubated in hybridization buffer at 65° C. for atleast 2 hours, the buffer is replaced with 10 ml of fresh buffercontaining the probes. After incubation at 65° C. for 18 hours, thehybridization buffer is removed, and the substrate is washedsequentially under increasingly stringent conditions, up to 40 mM sodiumphosphate, 1% SDS, 1 mM EDTA at 65° C. To detect signal produced by aradiolabeled probe hybridized on a membrane, the substrate is exposed toa PHOSPHORIMAGER cassette (Amersham Pharmacia Biotech), and the image isanalyzed using IMAGEQUANT data analysis software (Amersham PharmaciaBiotech). To detect signals produced by a fluorescent probe hybridizedon a microarray, the substrate is examined by confocal laser microscopy,and images are collected and analyzed using gene expression analysissoftware.

Example XLI Complementary Polynucleotides

Molecules complementary to the polynucleotide, or a fragment thereof,are used to detect, decrease, or inhibit gene expression. Although useof oligonucleotides comprising from about 15 to about 30 base pairs isdescribed, the same procedure is used with larger or smaller fragmentsor their derivatives (for example, peptide nucleic acids, PNAs).Oligonucleotides are designed using OLIGO 4.06 primer analysis software(National Biosciences) and SEQ ID NOs: 1-163. To inhibit transcriptionby preventing a transcription factor binding to a promoter, acomplementary oligonucleotide is designed to bind to the most unique 5′sequence, most preferably between about 500 to 10 nucleotides before theinitiation codon of the open reading frame. To inhibit translation, acomplementary oligonucleotide is designed to prevent ribosomal bindingto the mRNA encoding the mammalian protein.

Example XLII Production of Specific Antibodies

A conjugate comprising a complex of polynucleotide and a binding proteinthereof is purified using polyacrylamide gel electrophoresis and used toimmunize mice or rabbits. Antibodies are produced using the protocolsbelow. Rabbits are immunized with the complex in complete Freund'sadjuvant. Immunizations are repeated at intervals thereafter inincomplete Freund's adjuvant. After a minimum of seven weeks for mouseor twelve weeks for rabbit, antisera are drawn and tested forantipeptide activity. Testing involves binding the peptide to plastic,blocking with 1% bovine serum albumin, reacting with rabbit antisera,washing, and reacting with radio-iodinated goat anti-rabbit IgG. Methodswell known in the art are used to determine antibody titer and theamount of complex formation.

Example XLIII Screening Molecules for Specific Binding with thePolynucleotide or Protein Conjugate

The polynucleotide, or fragments thereof, are labeled with ³²P-dCTP,Cy3-dCTP, or Cy5-dCTP (Amersham Pharmacia Biotech), or with BIODIPY orFITC (Molecular Probes, Eugene Oreg.), respectively. Similarly, theconjugate comprising a complex of polynucleotide and a binding proteinthereof can be labeled with radionucleide or fluorescent probes.Libraries of candidate molecules or compounds previously arranged on asubstrate are incubated in the presence of labeled polynucleotide orprotein. After incubation under conditions for either a polynucleotideor amino acid molecule, the substrate is washed, and any position on thesubstrate retaining label, which indicates specific binding or complexformation, is assayed, and the ligand is identified. Data obtained usingdifferent concentrations of the polynucleotide or protein are used tocalculate affinity between the labeled polynucleotide or protein and thebound molecule.

Those skilled in the art will appreciate that various adaptations andmodifications of the just-described embodiments can be configuredwithout departing from the scope and spirit of the invention. Othersuitable techniques and methods known in the art can be applied innumerous specific modalities by one skilled in the art and in light ofthe description of the present invention described herein. Therefore, itis to be understood that the invention can be practiced other than asspecifically described herein. The above description is intended to beillustrative, and not restrictive. Many other embodiments will beapparent to those of skill in the art upon reviewing the abovedescription. The scope of the invention should, therefore, be determinedwith reference to the appended claims, along with the full scope ofequivalents to which such claims are entitled.

We claim:
 1. An apparatus comprising a nanopore device furthercomprising: a film separating two pools of a medium, a nanopore providedin the film, wherein the nanopore is dimensioned for passing a polymertherethrough, electrodes arranged to apply an electric field between thepools, a measurement system configured and arranged to measure atransport property of the nanopore; and a finite state machineconfigured to control a property of the nanopore device and furtherconfigured to detect and control binding of a molecule to the polymer.2. The apparatus according to claim 1 wherein the finite state machinecontrols the nanopore device by means of voltage feedback.
 3. Theapparatus according to claim 1, wherein the finite state machine isconfigured to control the nanopore device to perform an analysis basedon the measured transport property.
 4. The apparatus according to claim1, wherein the finite state machine is configured to control thenanopore device by controlling the electric field applied between thepools.
 5. The apparatus according to claim 1, wherein the transportproperty of the nanopore is one selected from the group consisting ofcurrent, conductance, resistance, capacitance, charge, concentration, anoptical property and chemical structure.
 6. The apparatus according toclaim 5, wherein the transport property is the current flowing acrossthe nanopore.
 7. The apparatus according to claim 1 wherein themeasurement system is configured to measure the current flowing acrossthe nanopore through the electrodes.
 8. The apparatus according to claim1, wherein the finite state machine is configured to reduce thelikelihood of insertion of one or more additional nanopores in the film.9. The apparatus according to claim 1, wherein the finite state machineis configured to detect the insertion of one or more additionalnanopores in the film.
 10. The apparatus according to claim 1, whereinthe finite state machine is configured to control passage of the polymerthrough the nanopore.
 11. The apparatus according to claim 1, whereinthe transport property of the nanopore is current and wherein the finitestate machine is configured to detect obstruction of the nanopore basedon the current flowing across the nanopore.
 12. The apparatus accordingto claim 1, wherein the polymer is a polynucleotide comprising adouble-stranded segment and a single-stranded segment and the nanoporeis dimensioned to permit translocation of the single-stranded segment ofthe polynucleotide, but not of the double-stranded segment of thepolynucleotide, and the finite state machine is configured to controlthe nanopore device to draw the single-stranded segment of thepolynucleotide through the nanopore until the double-stranded segment ofthe polynucleotide is detected.
 13. The apparatus according to claim 12,wherein the finite state machine is configured to control the nanoporedevice to draw the single-stranded segment of the polynucleotide throughthe nanopore by controlling the electric field.
 14. The apparatusaccording to claim 12, wherein the finite state machine is configured todetect the double stranded segment of the polynucleotide based on themeasured transport property.
 15. The apparatus according to claim 12,wherein the polynucleotide is a DNA hairpin.
 16. The apparatus accordingto claim 1, wherein the transport property of the nanopore is current,and wherein the nanopore device further comprises a detection andactuation circuit configured to apply a voltage across the nanopore andto measure the current across the nanopore, the finite state machinebeing configured and arranged to control the detection and actuationcircuit.
 17. The apparatus according to claim 1, further comprising aplurality of nanopore devices and a plurality of finite state machines,wherein each of said plurality of finite state machines is associatedwith one of said plurality of nanopore devices, and wherein each of saidplurality of finite state machines are configured and arranged tocontrol the respective nanopore device to perform an analysis using thenanopores independently of each other.
 18. The apparatus according toclaim 17, further comprising a serial interface and addressable logicconfigured to multiplex data entering and exiting the plurality offinite state machines.
 19. The apparatus according to claim 1, whereinthe finite state machine is implemented in a field programmable gatearray.
 20. The apparatus according to claim 1, wherein the finite statemachine is implemented in a digital logic circuit.
 21. The apparatusaccording to claim 1, wherein the finite state machine is configured toreact to events on the order of a microsecond.
 22. The apparatusaccording to claim 1, wherein the nanopore device further comprises twochambers separated by the film, the pools being provided in each of thechambers.
 23. The apparatus according to claim 1, wherein the polymer isa polynucleotide.
 24. The apparatus according to claim 23, wherein thepolynucleotide is DNA or RNA.
 25. The apparatus according to claim 1,wherein the nanopore has a diameter of between about 0.5 nm to about 10nm.
 26. The apparatus according to claim 1, wherein the nanopore has adiameter of at most 10 nm.
 27. The apparatus according to claim 1,wherein the nanopore has a diameter of at least 0.5 nm.
 28. Theapparatus according to claim 1, wherein the nanopore is a pore orchannel.
 29. The apparatus according to claim 28, wherein the pore orchannel includes a biological molecule, a synthetic modified molecule,an altered biological molecule, or a combination thereof.
 30. Theapparatus according to claim 1, wherein the nanopore has a biologicalactivity.
 31. The apparatus according to claim 1, wherein the nanoporeis sized and dimensioned to allow passage of an activator or a cofactor.32. The apparatus according to claim 1, wherein the nanopore comprises abiological molecule or an altered biological molecule.
 33. The apparatusaccording to claim 1, wherein the film is a solid state membrane and thenanopore is a pore formed therein.
 34. The apparatus according to claim1, wherein the film comprises a compound having a hydrophobic domain anda hydrophilic domain.
 35. The apparatus according to claim 1, whereinthe film comprises a phospholipid.
 36. The apparatus according to claim1, wherein the polymer is DNA and the molecule binding to the polymer isselected from the group consisting of a complementary nucleic acid, ahairpin portion of the DNA, and an enzyme that binds DNA.